I don’t know if this info will be of use to anybody, but I thought I’d add it.
I neglected to uninstall the existing version before running the install for 4.1, and not all of the new features were functional. Uninstaller apps were available for both versions in the “C:\Program Files\MyEclipse\MyEclipse-UninstallerData” folder, and both produced an OutOfMemory error when I ran them, making it impossible to uninstall and start over. The heap size is set in the “Uninstall MyEclipse Enterprise Workbench v4.1 Milestone 2.lax,” and doubling it allowed both to run.
Great job on this release, and MyEclipse in general, btw!