From the screenshots this doesn't look like a colour order problem at all. There's no way you can get yellow from both red, blue and grey with just a messed up colour order. Also, the problem is probably driver related rather than a generic problem in the OpenGL implementation, so it very likely only happens on R200.

When it comes to OpenGL problems, "help me help you" applies as usual. The easier you can make it for me to reproduce and identify the problem, the more time I have to actually fixing it and the more likely it is that a fix actually happens. So if you do the following things, it would help a lot towards getting this problem fixed:

1) Test it on a different driver (ie, r300) and see if the problem occurs there as well. It probably doesn't, though.
2) If you know a MorphOS beta tester, get him to test on a recent MorphOS beta to make sure that the issue hasn't already been fixed, however I don't think this one has.
3) This is the most important step. Turn the problem into an as simple C code example as possible. Do the required OpenGL setup to reproduce the problem and draw a single primitive to display the issue, and then make the source code for that test app available to me. Bonus points if it uses GLUT for easy compilation/testing on Linux.