This is so true - you see this kind of thing constantly where somebody has inadvertently changed the way something looks and are suddenly lost. I think one of the defining characteristics of a good IT guy is knowing a bunch of different ways to do the same thing on the software their organization uses (be it the OS or the word processor or whatever).
since there's no way reach standardization on every little arbitrary piece of ui functionality, the best way to deal with this is to provide some "Emulate x" options in the menu, which would switch things around to emulate some other application X.
This problem lessens significantly once you decide the difference between an "issue" and a "detail".