Groudon: ...? I've got a hunch as to your problem. I could be way off, but if you're like the others on TSC that have had SonED crash on their savestates, then you're likely forgetting the same important fact.
All of TSC seems to favor Gens+ over every other emulator. But, by default, Gens+ COMPRESSES its savestates, so SonED can't read them. If you want to use Gens+, you'll need to disable the Compress Savestates option.
If you can get used to SonED, it's a simple step to learn SonED2, and you'll have much more editing power. I plan to make a Flash vid on how to edit layouts in SonED2 soon, so a few problems might be cleared up soon.