There's diferences, I've taken shots and sent them to Flask's author with detailed descriptions of them and he said there was definately an issue and it would be looked into. Quite a few other people have commented on quality differences to me as well, both before, and alot more after I wrote the letter mentioning it to Tom.
I also said the difference varies from source to source. Aliens, for one, has very little difference and in fact I've done quality comparisons on it recently and you're right it's not much different. Why? Because it's not a very recent movie and if you watch you can spot the analog artifacts they still have in it from when the DVD was mastered. This tends to be actually LESS of a problem than near-perfect copies because the random noise tends to break up iDCT "errors" that cause artifacts.
I've also got one of the newer "optimized" versions and it's running close enough to MMX speed with a FPU algorithm that I don't see much of an appeal to run MMX anymore. I'm betting by the time everything's done there will be several high speed and high quality decoders to pick from, definately a new x87, 3DNow!, possibly SSE1 and SSE2, maybe a new fixed point 16bit (was mentioned by the lead coder on the AMDzone version), maybe a rewritten MMX by Flask's origional author, etc.