Well I couldn't resist, I just had to play with it some more. It does seem like you can have docks on the left and top and not cause a problem with video software (in my case ATI TV and WinDVD) if you follow some guidelines. I'm just talking about untabbed docks here, and only the docks on the left and top:
1. Had no luck at all with any dock at Position: Left / Alignment: Top, or Position: Top / Alignment: Left. Both those arrangements caused the conflict no matter what I did with them.
2. Having the "Magnification" feature in ObjectDock's Appearance section enabled seems to be a major source of the conflict. I had a lot better luck with that disabled. I even tried smaller sizes such as 32 magnified to 64, or even 64 magnified to 64 (not a typo, I tried "magnifying" to the same size). The autohide and background transparency features didn't seem to be a problem for me. Also, I could use the same dock with the Icon Size set to 192 and magnification disabled and it wasn't a problem.
3. Total pixel size of the dock can be an issue. While I was playing with a dock at Position: Left / Alignment: Bottom the conflict materialized after adding a 10th dock entry at 64 pixels or a 7th dock entry at 96 pixels, both of which coincided with the dock crossing over into the top half of my screen (1600x1200 resolution). When I put an even larger dock at Position: Left / Alignment: CENTER though it wasn't a problem.
So if you want some docks on the top and/or left, are inclined to play a bit, and don't mind giving up the zooming, you can probably get it done. I'm a big fan of the zooming though, so I'm inclined to just leave the docks at the right and at the bottom. I'm sure there's more to it than this, for example I know when I first created a new default dock on top center or left center with the magnification enabled it wasn't a problem initially, but it always seemed to turn into one pretty quickly. I also found that I needed to quit ObjectDock frequently while wrecking it, probably to free up the resources Septimus referred to above. And the occasional reboot helps too - any of that software seems to get a little cranky after I start it up and shut it down a dozen or so times.
So that's about it for me. All this tinkering has made me want to watch a movie on my computer. Good luck to those who follow.