Just took the new release of 0.4 from your site - told it where my projects where (as usual) - got this:

Stack Trace: java.lang.RuntimeException: Failed to upgrade C:\Developments\build\work-directory\build-dir\allbuilds\allbuilds.xml
at com.atlassian.bamboo.upgrader.VersionOneToVersionTwoUpgrader.updateBuildFile(VersionOneToVersionTwoUpgrader.java:91)
at com.atlassian.bamboo.upgrader.VersionOneToVersionTwoUpgrader.upgrade(VersionOneToVersionTwoUpgrader.java:45)
at com.atlassian.bamboo.upgrader.DefaultVersionUpgrader.updateToCurrentVersion(DefaultVersionUpgrader.java:103)
at com.atlassian.bamboo.persister.file.FileBasedPersister.updateToCurrentVersion(FileBasedPersister.java:243)
at com.atlassian.bamboo.ww2.actions.setup.FinishSetupAction.execute(FinishSetupAction.java:47)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.opensymphony.xwork.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:365)
at com.opensymphony.xwork.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:217)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:191)
at com.opensymphony.xwork.interceptor.DefaultWorkflowInterceptor.doIntercept(DefaultWorkflowInterceptor.java:137)
at com.opensymphony.xwork.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:81)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.validator.ValidationInterceptor.doIntercept(ValidationInterceptor.java:115)
at com.opensymphony.xwork.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:81)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.webwork.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:171)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.atlassian.bamboo.ww2.interceptors.BasePermissionCheckInterceptor.intercept(BasePermissionCheckInterceptor.java:38)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:151)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.atlassian.bamboo.ww2.interceptors.BuildAwareInterceptor.intercept(BuildAwareInterceptor.java:56)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.AroundInterceptor.intercept(AroundInterceptor.java:31)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.interceptor.ExceptionMappingInterceptor.intercept(ExceptionMappingInterceptor.java:100)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.atlassian.bamboo.ww2.interceptors.SetupCheckInterceptor.intercept(SetupCheckInterceptor.java:29)
at com.opensymphony.xwork.DefaultActionInvocation.invoke(DefaultActionInvocation.java:189)
at com.opensymphony.xwork.DefaultActionProxy.execute(DefaultActionProxy.java:113)
at com.opensymphony.webwork.dispatcher.DispatcherUtils.serviceAction(DispatcherUtils.java:233)
at com.opensymphony.webwork.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:198)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:118)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:52)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.opensymphony.webwork.dispatcher.ActionContextCleanUp.doFilter(ActionContextCleanUp.java:78)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.bamboo.filter.BambooAcegiProxyFilter.doFilter(BambooAcegiProxyFilter.java:21)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.bamboo.filter.LicenseFilter.doFilter(LicenseFilter.java:71)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.johnson.filters.JohnsonFilter.doFilter(JohnsonFilter.java:91)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:83)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.seraph.filter.LoginFilter.doFilter(LoginFilter.java:91)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at org.springframework.orm.hibernate.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:174)
at com.atlassian.spring.filter.FlushingSpringSessionInViewFilter.doFilterInternal(FlushingSpringSessionInViewFilter.java:29)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:77)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at com.atlassian.bamboo.filter.CompressingFilter.doFilter(CompressingFilter.java:69)
at org.mortbay.jetty.servlet.WebApplicationHandler$CachedChain.doFilter(WebApplicationHandler.java:823)
at org.mortbay.jetty.servlet.WebApplicationHandler.dispatch(WebApplicationHandler.java:473)
at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:567)
at org.mortbay.http.HttpContext.handle(HttpContext.java:1565)
at org.mortbay.jetty.servlet.WebApplicationContext.handle(WebApplicationContext.java:635)
at org.mortbay.http.HttpContext.handle(HttpContext.java:1517)
at org.mortbay.jetty.plus.PlusWebAppContext.handle(PlusWebAppContext.java:158)
at org.mortbay.http.HttpServer.service(HttpServer.java:954)
at org.mortbay.http.HttpConnection.service(HttpConnection.java:814)
at org.mortbay.http.HttpConnection.handleNext(HttpConnection.java:981)
at org.mortbay.http.HttpConnection.handle(HttpConnection.java:831)
at org.mortbay.http.SocketListener.handleConnection(SocketListener.java:244)
at org.mortbay.util.ThreadedServer.handle(ThreadedServer.java:357)
at org.mortbay.util.ThreadPool$PoolThread.run(ThreadPool.java:534)
Caused by: java.io.FileNotFoundException: C:\Developments\build\work-directory\build-dir\allbuilds\allbuilds.xml (The system cannot find the file specified)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(Unknown Source)
at com.atlassian.bamboo.upgrader.VersionOneToVersionTwoUpgrader.updateBuildFile(VersionOneToVersionTwoUpgrader.java:74)
... 85 more

FYI - this ain't the right folder - C:\Developments\build\work-directory\build-dir\allbuilds\allbuilds.xml
Should be C:\Developments\build\work-directory\build-dir\allbuilds\download-data\rss\allbuilds.xml