The processor on the 505 is not fast enough to catch up with the tr-909 style programming. Plus you have to remember that the 505 is a midi instrument, so it has to register the keypress into sequencer memory b4 it can process the sound. The 909 is pure analog, so it has no latency issues. As for the clock timing thing, I really have no Idea. I've had mine since 1998, and it's only major problem is 2 bad crashes. (But I had memory card backup the second time.)
I'd say backup your data and maybe try a factory init. There is a new OS on the roland website, but as far as I can tell--adds nothing. It is possible that you may also have a bad OS installation, so if the factory preset doesn't work, you'll want to try that. Also make sure that when you mess with parameters that you're not on MEGAMIX, and that you are not accidently hitting preset patterns when you mix.
--XeNO
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"Blasphemy is a victimless crime."