Update to 6.31, the latest public release. Though I don't know if this'll fix your color problem, it's worth a try. 6.40 is a public beta so it'll have bugs (beta normally means bugs), but 6.40's MED has quite a few new features to it, including support for true color in the skin edittor. Beware though, if you pass 16 groups, MED will crash. I don't get why it's taken so long to fix this bug - I reported it nearly 3 months ago....

As to the animations, I've run into this problem myself, the rotating of bones anyway. I practically haven't done any animations in MED so I otherwise lack experience. I can otherwise form nearly anything, given calculations.

Edit: The update is free. 6.40 is in the updates and announcements forum.