Do you have Perian installed? I had what sounds like a similar stuttering effect when I used Log & Transfer from an AVCHD camera a couple of months ago – I tried everything, and then stumbled across the notion that Perian messes with Quicktime in some incomprehensible-to-me way when one is trying to work with .mts files. I uninstalled Perian, and everything worked perfectly after I re-L&Ted.
I realize you’ve got a different workflow, but if you’ve got Perian, it is a prime suspect.