I seem to recall having a similar problem with my FUSS derivative while trying to get the dynamic command support to work, and I believe it was somehow related (i.e. the commands no longer working after a copyover). Wish I had better news for you, but I'm not remembering any kind of resolution, at least not in my case.
For what it's worth, I'd be surprised if the two were not related somehow, based on your description of the problem. Then again, this might be a simple makefile issue, since I doubt most AFKMud users have this issue or it would have been prevalent before.
Check the makefile options and see if you missed something, otherwise it might be a Cygwin specific issue (I was also using Cygwin).
Hope that is even remotely helpful.