First I was just amused by the fact that he had curtains, because I had never noticed them before. But last night, they just grabbed me. Curious, I busted out my Season 3 DVD sets, and in the middle of the "Tao of Rodney" commentary, we finally got the scene between John and Rodney and the ascend-o-meter, and there they were in the background. So now of course I'm going to have to look at the evolution of Sheppard's curtains (because I'm that much of a dork). Anyway, the curtains in "Tao" are most certainly different. They're more of a rough fabric, not really hung in any real pattern, it's like they were put up as an after thought.
Apparently at some point between Rodney's ascension and finding a new planet, John hired an interior decorator.
In "Doppelganger", the curtains aren't... well they're not frilly, but they are not the manly curtains of Season 3. But it's like Teyla went out shopping and bought them at the Pegasus Bed, Bath, and Beyond, then hung them, and tidied up the place a little while she was at it. The curtains have actually been moved to a functional place in front of the window, and in addition to the functional ones that might block out light, someone thought to hang, oh, what the heck are they called, the ones that you drape on top, just for pretty effects?
I've got a fairly big TV so I can see them, perhaps a little better than intended. It could be the night light, but first off they're sheer and see-through, and maybe it's just the night lighting and the blue light they're casting, but they look purple (okay, maybe a dark lavender), and they sparkle.
I think it was the purple and sparkliness of them that made me have to rewind and watch the scene, actively trying not to look at them.
ETA: Went and rewatched the McKay/Shep scenes in "Tao" (such an imposition, I know), and in the day scene it was easier to see the curtains. I still maintain they are different curtains, but I will admit they were also sheer, which takes away from their rugged manliness some.