The most likely reason is that it's not a fully qualified path - it's a relative path, and I've seen this before as an intermittent problem with VS builds. Changing to a full path:
CALL "C:\MyApps\CopyFilesToProducts.bat"
should cure it.
I suspect that the "current folder" that VS uses as the starting point for the relative path specification depends on the last operation it needed to do as part of teh actual build operation, but I'm not sure.