i have experienced a similar problem as this. i was trying to record MIDI keyboard while rewired with audio. a suggestion i got was to look at the audio card you are using. there are certain cards that work amazing for playing back music etc and sound great, but they are not very good at all as far as recording goes. it really messes around with your system latency and causes information to be really screwed around with.
you can also try adjusting your buffer settings. this will give u smoother performances with bigger latency, or less latency with not as "smooth" of performance. whatever that means.... maybe give it a try if u havnt yet.
anyway, hope it works out.