It should switch from one to the other seamlessly (well, I mean in that it'll automatically load up the bit in question). Have you tried running the developer's version? I always just use that even though I never use the cheaty bits during actual gameplay. The number of saves certainly shouldn't make a difference. Worst case it may still be possible to send one off to support for them to look at. Raze will probably look in at some point, if not I'll ping him! Edit: which I've done anyway.
I contacted support. I haven't tried the developer's version, maybe I should check it out. Also thinking of choosing ' Flames of Vengeance ' from the menu when game starts, maybe that will make a difference, I dunno. Because maybe the game thinks I am still running through Ego Draconis? After I deleted the 2 extra save files I had no crashes for a good amount of time and then it happened in crow's nest again. Expansions tend to be buggy, there was a similar issue with Doom : Resurrection of Evil or maybe it was just me.