thumbFilePath shows full file path for some records
The simplest option would probably be to make a backup of the uploads table, open the backup file in a text editor and run a search/replace to make the paths relative, then restore from that backup. I'd also keep a copy of the original backup just in case something goes wrong with the search/replace.
Alternatively, if the discrepancy is causing issues on the front end because the paths aren't consistent, there's a CMSB function called realUrl() that converts relative URLs to absolute and leaves absolute URLs unchanged. Using this on the path before display would convert it into a consistent format.
Let me know if you have any other questions!