Actually I've been seeing the same problem. Almost gave up on fixing it....
My configuration is like this
D-SUB----------VGA breakout cable---------------HDTV
DVI--------------DVI2VGA Adapter-----------------CRT Monitor
I use BBA Radon 8500 with Catalyst3.0, and the way display scheme is setup is,
PC_mode: Only DVI-port(VGA through adapter) is enabled, and hence primary.
TV_mode: Both ports are enabled and D-Sub port is primary, and DVI port is secondary clone mode.
I always wondered why I see flickering scan lines on my monitor only, which is always through the adapter. But was not able to solve it and gave it up.
Recently, I ran 3DMark benchmark, and leared that if I just use D-Sub connected to CRT monitor(pretty normal PC use), I do not see these problesm and gets great score. But as soon as I configure it like above, which is a must for me, I do see this scan line problem (very annoying) on the monitor, and worse, my 3DMark point decrease by 60%. :Q
I am not a big fan of 3D game, but still like to use my video card correctly and achieves the high 3dmark score, dont ask me why. So I am again searching the web to see if there are any other people who has had this problem. No I dont think it is monitor sitting too closely, because my TV is like 20 feet away from my PC. I think it has to do with video card not being able to perform well when used with DVI2VGA adapter. But who knows... Maybe those DVI-I and DVI-D issue ?