You ask what the difference is when transfering MiniDV to PC via Firewall, but don't mention the other way we are supposed to comment the difference of.
OK, So you have your MiniDV cam plugged into the firewire port, right?
Then you bring up your software, (Which software is it?) and choose import from device, right?
Are you sure you are importing to the new drive?
What size is the video you're bringing in? 740x468, 320x240, etc?
Are you bringing it in as an AVI, or MPEG file?
Is it compressed or uncompressed?
Have you run a diagnostics on your PC to see if there are any conflicts?
Basically, you plug the firewire cable into the cam, then into the PC. Then turn on the cam and start the application. I use Sony Vegas. Then you choose import video. I start the cam and walla... it's importing. Although my drives are different than yours, it should be pretty much the same.
I don't know if it would be a problem, but what kind of graphics card do you have? Is it built into the mother board or do you have a separate one?
One other thing I just thought about is the sound... We've been talking about the video, but there's a sound track on there too. What are you doing with it? What compression are you using to handle the sound, if any?