Bob,
I assume you’ve installed MyEclipse as administrator (or using sudo). This isn’t recommended. However, In this case, the configuration location pointed to by -configuration may not be writeable by users. You will have to make that configuration folder writeable by the users you want to access it. I guess, moving the configuration folder to a writeable location might also work.
-initialize is a standard eclipse parameter and doesn’t take arguments, so you should be able to just add it, if you want to. It’s not an option I’m familiar with but the eclipse help shows that the IDE will not be run if it is included; it merely reinitializes caches and structures.
Please let us know if this helps.