Using the -clean command line argument when starting up MyEclipse can help with problems related to stale plugin cache information (usually shown in the log as problems loading bundles). The way it is used is as an argument to the MyEclipse executable; on Windows that is myeclipse.exe, on Linux or OS X it is myeclipse:
On OS X, the path to the executable is complex, so this may be an easier way to start MyEclipse from the command line (assuming it was installed into Applications):
|open /Applications/MyEclipse\ Professional/MyEclipse\ Professional.app --args -clean
Alternatively, add the following line to the myeclipse.ini file, near the top:
Refer to the FAQ here
for how to locate the ini file.
If you have installed MyEclipse as a plug-in to a classic eclipse installation, the corresponding executable is eclipse.exe and the ini file is eclipse.ini.
This option tells eclipse/MyEclipse to erase and rebuild its plugin cache to avoid conflicts with incorrect plugin information. This is very important to use when upgrading between major releases or trying to fix a strange behavior in your workspace. After you have used -clean once, you are free to remove it from your command line arguments. Indeed, it's recommended to remove it, since startup takes noticeably longer with -clean.
Another good resource on understanding -clean as well as other methods of restoring a defunct workspace are in an EclipseZone article here