It looks like when I said that the MPEG-2 compression did not affect the red/blue 3-D effect, I was wrong. I've had time to make a test disc and try it out on my progressive scan 16x9 TV and two other standard def NTSC television sets, and in all three cases we have massive ghosting - so much so that the anaglyph movie is almost unwatchable.
How did this happen?
My original test movie was rendered out from After Effects via the Windows Media 10 codec, and streamed to my TV via the Xbox 360 - and it looked perfect. The best red/blue 3-D I've ever seen on a television. (This version, incidentally, will be made available for download - likely via BitTorrent.)
This new version is rendered out via After Effect's MPEG-2 compressor, and it appears that it has subtlely altered the shade of red. This MPEG shade is darker than it needs to be, so the red eye of the glasses can't filter it out properly, resulting in double images.
Yesterday, I went and rendered out another MPEG 2 compressed version. For this one, I cranked the Red Gamma of the left eye channel up from 1.5 to 2.0 (a significant difference.) When I tested it on my home TV, it actually did work much better. Not quite 100% ghost free, but acceptable. The downside is that all color information is completely lost. The movie is basically purple, and the red eye version is starting to get a bit washed out.
I've sent this disc home with Andy for testing on a standard TV, so we'll see how he says it works. In the mean time, I got to thinking that since the luminance of the red needs to be brighter, what would happen if I increased the Red Gain instead of the Red Gamma? So, I've rendered out yet another version! This one resets the gamma to 1.0 but boosts the red luminance, resulting in an extremely bright red. The image retains more of the original color information, so hopefully I'm on to something that will work.
Unfortunately, I'm out of DVD-Rs at the moment.