We have a plan that's set to build off the branch 'firewalled-magnets-v4-branch' (with the module 'limewire'). Bamboo seems to be listing the correct changes, but not actually updating the files. Looking at the one of the CVS/Entries files in the build-dir for the plan, it looks like Bamboo just didn't checkout the correct branch. The Entries is listed as if it were MAIN (no branch information included). Some relevant lines from the logs:

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2008-04-04 02:32:06,152 INFO [BAM::Default Agent::Agent] [AgentQueueAccessorImpl] LW-MAGNET-73 taken from queue.
2008-04-04 02:32:06,153 INFO [BAM::Default Agent::Agent] [DefaultBuildExecutionManager] Plan 'LW-MAGNET' started on agentId 65537
2008-04-04 02:32:06,155 INFO [BAM::Default Agent::Agent] [BuildAgentControllerImpl] Build LW-MAGNET-73 started building on agent Default Agent
2008-04-04 02:32:06,155 INFO [BAM::Default Agent::Agent] [DefaultBuildAgent] Running build task: com.atlassian.bamboo.v2.build.task.CheckoutUpdateForBuild
2008-04-04 02:32:06,156 INFO [BAM::Default Agent::Agent] [CheckoutUpdateForBuild] Updating source code to revision: 2008-04-03 17:21:25 -0400
2008-04-04 02:32:06,249 INFO [BAM::Default Agent::Agent] [CvsRepositoryManager]
Running CVS command: 'update -d -P -D 2008-04-03 17:21:25 -0400 '<br />
... in: '/n/bin/bamboo/data_20/xml-data/build-dir/LW-MAGNET/limewire'<br />
... CVSROOT: ':ext:bamboo@cvs.limewire.org:/cvs'
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Not sure if the branch name should be listed there (but it isn't).