Draeka,
If you get an error like that you need to make sure to answer YES to ignore it, otherwise the CK will crash. (I think that's the right one). Same thing happens to me the first time I try to add any conditions on Perks, and Magic Effects. Very annoying if you lose your work because of it.
Edit: Sorry... I just reread your post...apparently more accurately. You mentioned:
Even if I hit 'Yes To All' once I'm done editing and hit 'OK' the CK crashes and my changes are lost.
Once you're done editing, what does your condition look like before you hit OK?
-MM