I have the same issue at times. Sometimes I can do it just fine without feeling weird, other times it doesn't feel right and I wonder if I look strange. At those times, I usually just walk with my hands in my pockets and ocassionally pull them out to see if I can pull off the hand movements fluidly. It doesn't really concern me that much but if it's a real problem for you, you could try walking in front of a full-length mirror or video tape yourself. Then either watch it and judge the movements yourself or compare it to YouTube videos of other people walking. I hope this helps.
Edit: I noticed a post above me suggested not swinging your arms at all. If you don't care about how you look (you're around people you'll probably never see again), then go for it and don't waste the effort. But failing to conform around NTs that don't understand your situation (and that you want to socialize with) could hinder you.
Edit: Actually, one benefit to doing it all the time, even when you don't have to, would be getting more practice at it, that may make it worth the effort.
Last edited by jlharrison on 01 Jan 2011, 6:47 pm, edited 3 times in total.