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If you perform an evaluation and then move a file like a source file, a test input file etc. (to replace an old file, or to add it in the first place), the evaluator might not notice the change when it is run again. This is because a move operation preserves the file's time-stamp, so the modify time might very well be before the time of the original evaluation. Unfortunately, fixing this problem would probably make the software much slower. To avoid this problem, always copy a file to a directory under eval/ (as opposed to moving it from some outside directory).
Under Windows, a fatal error might occur if the system is under heavy load. In this case, eval will stop with the following message: FATAL ERROR: shoot! Cygwin bug...
This is likely a bug in the Cygwin DLL (the pid management code). Hopefully, this will not cause problems, since the grading machine is not normally under such a heavy load.