Other than the fact that they share home directories they really weren't linked up.
I've since moved both accounts that had troulbe to local home directories (on each mac). I haven't noticed the issue and I don't think my wife has either. Unfortunatley one thing I also did at the same time (well the night before) was remove our ~/Library/Fonts directory from each persons respective home directory. I'm not sure which solution fixed the problem
I'll re-post if I see the issue again. I'm thinking it was related to some corruption in that Fonts directory, whether it was caused by some wacky NFS issue I can't say.
Clarification: when I say 'they share home directories' I mean that both users had their own individual home directories, but they were located on a NFS file server. So the users themselves weren't sharing home directories with eachother, but between two machines.