I have an unmodded,unpatched version (which reminds me i better start downloading soon,excellent stuff around here),and i used to get crashes to desktop when loading games as well.
The catch in this whole thing is that i used a save slot when in contact with the enemy and another one when in transit,overwritting as necessary. Due to the game erasing all the in-mission saves except the one you load,i have lost 2-3 carreers with 1-2 patrols completed each,as ALL of the in base saves got corrupted as well
Some time later i stumbled upon this forum,and i saw other people had the same problem too,and they had updated versions of the game,so it was probably not something a patch would fix. As someone suggested,i started the practice of NEVER overwritting a save game,but numbering a succession of save games according to what i'm doing (e.g transit1,transit2 and so on)
Up to this point i haven't had any saves corrupted,so it looks like it's working. Just in case,i backup my saves anyway,so i can reload a previous one if another one refuses to load.