My guess is the flicker is caused my your Toshiba(which are known to be very trigger happy AFA CP detection) falsely detecting a CP signal(change in lighting would be a good example of a area that might trick the recorder).
As you noted, just routing your signal through your Toshiba can cause problems because of the design of the machine. I had the same thing happen when I first got a DVD player. Because my TV didn't have a video input(and that's all the DVD player outputted) I had my DVD player running through my Samsung VCR. Even though I wasn't recording with the VCR I got bright and dark flashes when playing a CP'd DVD
Non CP'd DVDs played just fine.
In desperation I tried a older Samsung VCR I had and it allowed pass through just fine although as expected if I tried to record the DVD my output would start flashing dark and bright. I guess the point of my story is that depending on design, even pass through can exhibit the same signs of trying to record the signal.
I know you said your DVDs aren't CP'd but some machines(Toshiba, Sony and JVC jump to mind) are designed so
fussy that they can detect a CP signal even when they aren't present.
A couple of choices for you would be: A) get another DVDR that isn't overly trigger happy(Panasonic or one of the Magnavoxes w/hdd come to mind) or B) purchase a video filter to remove CP(or what your Toshiba is thinking
is CP). If you have the option my first suggestion would be to get another brand DVDR. Every filter I've ever tried messes with the black level a little. It sounds like you're a bit on the fussy side
and you may not like the increased black level(blacks not being totally black) I know I don't like it
For a list of current and past Panasonics click my signature. For info on the Magnavoxes, check Wajo's sticky thread for a wealth of information.
For information on video filters
you can check out any of the many threads talking about those.