I noticed that my save files were getting to the point of 1 gig after playing through newgame+ the 8th time (yes, my character is so strong right now she has no difficulty whatsoever; that's the appeal for me playing through so many times). So, to spare you (you, the one other person as crazy as me) the pain of losing so much JE progress, I'm sharing my fix.

The problem for me was the KillList was becoming unwieldy with too many duplicates, so, the fix to apply (ideally before your save file gets to be 1 gig, otherwise you get to use Perl on windows for two hours trying to recover your save):

1. Download K-GFF and SAC Utils from: http://jadeempire-modding.wikia.com/wiki/Tools
2. Extract both into the folder of a save that's getting bloated (example: "Jade Empire\Save\Auto 24 - 2h 19min - level 7")
3. Click and drag save.sac onto sac_dump.exe
4. Click and drag save.sav onto kgff.exe
5. Navigate in K-GFF to STRUCT ID -1 => PlayerCreature => STRUCT ID: 0 => Progress => STRUCT ID: 0 => KillList
6. Right-click and select Delete Field
7. Save the save.sav file, and close K-GFF
8. Run sac_fill.exe
9. Rename new_save.sac to save.sac (file size of a healthy savefile in JE is about 1 to 5 MB)
10. Enjoy the fact you can no longer read loading or saving screens due to how fast those actions happen