I do it before I start DVHSTool. It's like a ritual that I have to perform for some reason, or else it fails for me. I turn on the 30k, turn it off, turn it on again, turn it off, turn it on again, turn it off, then turn it on and run DVHSTool and start the transfer. It's a pain in the ass, but it works! If I only cycle it two or three times, it doesn't work. I've tried restarting the computer, manually resetting the I number on the 30k, but only the recycling seems to work. This is with a new 30k (newer serial with the upgrade) using JVC D-VHS 300 tapes.
Anyways, good luck.