Bamboo ignores CVS error messages and updates on wrong files, and reports "Update By Unknown" in the changes tab

Bamboo cannot handle the CVS-Errormessages in the right way:

We have some Sourcecode generators during our ant builds. These generators also create some stubs, which are jsut generated one time and the developer has to implement them manually. After beginning the manual implementation, these files are checked in the CVS. Usually the check in of the model and the check in of the manual implementations happen in one step. Sometimes that is not possible.
At the build server bamboo creates now the stubs and puts them into the source-folder. Then the developer checks in the stubs at his own machine. At the next time Bamboo runs the plan, it wants to update that folder. But the CVS says (i.e.):

cvs update: move away src/de/xxx/xxx/common/components/clickandbuy/xxx.java; it is in the way
C src/de/xxx/xxx/common/components/xxxl.java

Bamboo recognizes the changed files but cannot get the history, because bamboo has just the wrong files... The Build should fail with the error message of the CVS...