Theoretically, the HDTV Wonder should work with ANY DX9 card. I don't have enough experience with it to say whether you absolutely need a Radeon (but since it would be an ATI-ATI combination, it's probably a better bet if since you are having problems). Remember that the reviews of the HDTV Wonder were also based on the ATI software, which may not play well with other video cards....Hard to say though if that is the root cause. I hate to recommend spending money to fix a problem that shouldn't exist, but you could buy a Radeon just to see if that actually resolves your problem, and return it if the problem is really something else.
As far as knowing when I'm dealing with a 1080i signal, I just know what my local stations are broadcasting. In general, FOX and ABC will be in 720P. CBS and NBC will be 1080i simply due to the fact that those are the network's standards. I can definitely corroborate the stuttering to the 1080i channels. I don't see it on 720P, so I'm assuming it has to do with the deinterlacing functions of the codecs.
Anyway, I have only used the TheaterTek codecs for MCE. I did watch a couple minutes of movies with TheaterTek app itself, but I haven't spent enough time with it to really comment on how good or bad it is. I do see that there is a 2.01 update, so I will download that and see if it happens to fix anything with the codecs.