It would manifest in any save file made after the offending mod(s) were first installed. In order to check to see for certain if it is a mod, you'd need a 100% vanilla save file made before any mods were used.That's what is strange on the whole ordeal. It would seam that whatever was wrong manifested in older saves aswel. Saves from last year, from version 1.52, from version 1,2 - very odd.
It could also be the installation itself. Sometimes mods or other factors will alter the actual installation files. This would definitely require a reinstallation unless the user knew exactly which files were affected. Verifying / repairing can't always fix this.
My steps would be:
1.) With all mods removed, verify/repair the installation.
2.) Back up all save files, and ensure the folder is completely empty.
3.) Begin a brand new game, Level 1.
See if any issues crop up there. If so, I'd cut right to the Clean Installation.