the glitches are happening on the fly right?
not in the HDV compressed files?
This reminds me of days long ago printing to video from adobe premiere 4
What I would do is when your all ready to do it,
shutdown the machine, wait a minute, then power it up.
launch fcp and go for it.
You might also look into a really high quality firewire cable
and get one as short as possible.
that might help.