what mods do you have installed. I had the same problem and it turned out to be mod related. The supermods like GWX and NYGM already add alot of additional data, so some of the additional mods you add may be overloading the game. I believe there is a limit to how much data can be processed by the game engine, so even though you may have a powerful system (as in my case) the saves will still get corrupted if overloaded. In my case FM's excellent new interiors mod was the culprit. Other large mods such as Aces super pens, and the harbor mods also may be causing this due to their large size
this has been discussed at length in other posts
bear in mind to some extent save game corruption is a bug feature in SH3 (also discussed in many threads) However, I am convinced that this happens much less frequently in unmoddified set ups thans it does in heavily modded setups. If anyone can confirm or deny this please do so