My error message is as follows:

File /tai/bamboo/bamboo-agent-home/xml-data/build-dir/INF-CLEAN-CC61/cleanuptask.xml was ignored because it was modified (2015-09-08 15:45:50.000) before task started (2015-09-08 15:45:50.513)

As you can see, the file time-stamp is only accurate to the exact second. Time stamps on the file system are truncated to the nearest second. Knowing when the task started is accurate to the millisecond. To compare one truncated number to a non-truncated number and that comparison causing a build failure is an unfair comparison.

I recommend you detect whether that file was created before the task started, by using the task-start-time by truncating both numbers, as defined by the file system.