When i first started training in Aikido I had the same problem, i found that i was getting extremely sore legs and had to frequently sit up slightly or shift my weight. I think the only cure is time and practice, mayby try sitting in seiza for 5 min everynight....also i no this is kinda hard but when you sit in seiza be as relaxed as possible, you need to get your muscles used to it and relaxing them makes it easier.
I know now i can sit in seiza for a long time and only feel little discomfort but its hard to stand up after it though, your legs feel like jelly
I think my biggest problem is my ankles now, if any one has advise or remidies for sore ankles when sitting or going into seiza please let me know....mayby all they need is time to but who knows!!!
i hope my advice helps a bit!!!