Problem:
Save games won't work anymore (and/or say that they are corrupted) after I installed Mod X or I have NanoFX installed (and/or started again).
Reason:
The BC save system records almost everything, including current HP condition, and it's max condition, and it will say that the savegame is corrupted when the newly loaded values (from the hp file) don't match with the values in the savegame because a mod has changed them.
With NanoFX there is something similar going on. NanoFX is very random by nature, so the values it records from the save game, and provided by NanoFX don't have to match, and result in a corrupted savegame.
Sollution:
Try not to use save games, but use select the mission you were on in the Custom Missions section (above the QuickBattle button) that part gets updated when you complete a mission. You might not get accurate HP results, but it's better than nothing.