Post more about your system. OS, versions of FCP and QuickTime you’re running and on which machine/disk array?
The transcoding is more so for sound sync, than the actual edit, so it is being done on a Macbook Pro Snow Leopard 10.6, FCP 7, QT
Oh also, I ran a test through compressor, same settings, and it didn’t have that lag, but I want to use Streamclip because it’s faster and Compressor only allows a limited amount of clips to be done at once when I tried it