Way back when... before there were a lot of mods for SH3 floating around, I used to have the very same problem with stock SH3. The cause turned out to be locked files in the career/scenario files that SH3 could not access due to some flavor of "Access Denied":hmm:
A possible fix posted at the time was to copy your save game files over to a new folder, delete the save game files that caused the problem, and then restore the originals from your copy. I have to admit that it didn't work so well for me, so I wound up deleting the save game files and starting a new career.
Did NOT have to reinstall. If this doesn't resolve the problem then I think the shortest route from here to there is the straight line of "format and reinstall" (borrowed, with acknowledgements to
www.microsith.com)