ttrammell sent me some more info and the issue is probably caused by 8.3 names (DOS names). One course of action would be to mangle all 8.3 names on the server, the other to advise people to turn off 8.3 name generation.
Let’s go with the second first: See here for how to do this: https://support.microsoft.com/en-us/kb/121007 . It has performance benefits as well.
I’ll add that link to the manual as setup step. The problematic pair of file names also should be rare such that it is improbable that many other people have this kind of problem, if they have not turned off 8.3 names.