I would recommend changing your USB latency to something higher, such as 5 or 10 and seeing if that makes a difference. If the Scratch Live audio has a drop-out, then often this also results in a small glitch in the audio recording, which will put the audio out of sync with the video. Also, perhaps reduce your ME cache size to around 500 MB and see if that has any effect. If you're not doing long loops, and your videos are all well encoded (i.e. they have keyframes every 20-30 frames), then there is not real reason to set the ME cache to some high number. I use ME with the lowest settings - mainly because I don't have a lot of free memory though. One other thing - if you are low of free memory, then try playing a few videos through before you begin recoding. This will make sure that there is enough free memory for ME to use in the cache, and reduce the likelihood of Mac OS from swapping any further memory to disk during your performance.
