I have more than twenty thousand multimedia files linked to my RM 188.8.131.52 database. The earliest ones are dated in 2001, which was when the prior program (Family Origins) was current. "Fix broken media links" has several times been very useful in correcting my mistakes - typically renaming or moving a file from Windows rather than than within RM. I would not suspect that the tool is broken, but I haven't got a clear suggestion of what your problem really is.
I learned, the hard way, that I need to be careful to give every media file a unique name. Early on I set up a folder organization to place birth, census, city directory, death, etc., etc. media files into separate folders. It was a carryover from how I organized files submitted by my students for evaluation and grading. Anyway, the mistake I made, early on, was to allow 2 files, stored in separate folders, to have the same filename. Bad idea. RM's "Fix broken media links" doesn't look at the path & folder when it is trying to resolve broken links. So RM tried to incorrectly link a bunch of my mistakenly-identically-named files. What a mess I had made. It has been years since I learned that lesson, and with thousands of media files, I am still finding duplicate filenames to sort out. Some days, even with 30 years of experience in genealogy, I still feel like a rookie.
I suggest that you look carefully at the drive & folder location of your media files. Check RM's Tools > Program Options and verify that the Folders are documented correctly. Make sure those folders are not in the boot drive's system folders. Make sure that the media folder(s) are not designated as Read Only (Windows - Properties - Details).