Yes I made sure the Line input was selected for recording.

And remember that it did work perfectly fine in ATI's own software.
Unfortunately my computer hates me. I did a test capture of a full 1 hour 50 minutes yesterday, and it captured fine (although I lose about 1 frame in a thousand, I don't know why, and yes everything else was shut down). Possibly this is due to IRQ sharing, which I hate but can't avoid because of the damn way that every system is designed these days.
Anyway, I started up the capture on the first airing, but then realized I hadn't checked a setting, so I stopped it and by the time I got back to it I'd already lost several seconds of the opening credits. No big deal I thought, because it was airing again immediately afterward. So I let the VCR record and just left the computer recording off.
11PM rolls around. VCR goes off, it worked fine. Since I had to work the next day, I figured I could set AVI_IO to record for 2 hours and 15 minutes, just to be sure I got it all. I started it a minute or so before the actual movie started again, it seemed to be going okay for about half an hour (though still losing a frame in a thousand, plus it lost a few more when I decided to do something that caused disk usage). So I shut off my monitor and went to bed. A couple of times I got up to check on something (since I usually read for a long time after getting in bed), and it was going fine. But I ended up going to sleep about 20 minutes before it ended recording.
I woke up this morning, turned on the monitor, and got the 'No Input Signal' warning. That's normal when the system sleeps due to no activity (or perhaps dozes is the correct term) and the system is still running, so I move the mouse expecting immediate response as usual. No response. Try again, click the buttons, nothing. Start hitting keys on the keyboard, nothing. Control Alt Delete...hard drives spin up...still no signal...tried C-A-D again, nothing...so I hard power cycled it. Boots up fine, there's the 27 initial files on the capture drive created by AVI_IO, all either 0 bytes or 2KB for the header info. No captured video of any kind. Whatever it got during the recording was completely lost and is probably a lost fragment right now and totally useless.
So, tonight I'll be recording episode 2 while I'm awake, and starting the encoding before going to bed, and tomorrow I will record episode 1 again off of VHS, assuming it's decent quality (haven't watched it yet). If it's crap, I'll wait for SciFi to re-air it next Sunday (I'll probably capture it again then anyway).
So of course my real problem is the lost frames. I don't know what might be causing them. It's not a lot, but it's certainly not 0% loss. I've got a Thunderbird 800 and 640MB of RAM, so I don't think the compression process is being bogged down since it's not all that extreme a compression going to HuffYUV, and I'd hope that the hard drives aren't the problem, given the speed they're able to pass data at (and even if they were a bit too slow, the system should be able to buffer a bit more to avoid losing frames). AVI_IO doesn't seem to have any options for buffer settings, but the IO Buffer item at the bottom during the capture never went above 3 of 50 for so brief a time I could barely see it.