Mike,
Thanks for your interest about M4M. MyEclipse 6.1 will actually include a fully updated version of Matisse that is synchronized with the NetBeans 6.0 release. You should see a lot of those issues resolved with this updated release. We should have Milestones of 6.1 beginning early next year, and the final release is due around March I believe. That way you could try it out and keep us honest, make sure we get those issues resolved before we ship 6.1 final if you had the time.