I found why this was happening to me. Back story is, I always preferred to use the File options (in prefs) "OS Native" which shows a windows window instead of a Maya window. Hated the Maya I/O gui for years, it was slow to populate on some servers and had trouble remembering my bookmarks (prolly due to work workspace practices and proprietary stuff).
Anywho, changed my settings back to Maya default for File preferences and my fbx batching script started working. I had tested resetting prefs and that worked, but then had the idea to try just the file related pref on a whim and sure enough that was causing some sort of conflict/ behavior that would block my script from running processes on multiple files in a folder. That is likely the issue for some others here. Probably why I often got naming coflicts/namespace errors on fbx imports regardless of settings. . .