bittersweetryan,
Can you answer some questions for me?
1) Can you share the build id from Help > About Blue Edition ? Paste it here.
2) Clear the contents of the .log file which is located at <workspace dir>/.metadata/.log. Now try starting MyEclipse without the -clean option. Copy paste the errors logged in the .log file here for me.
3) Is your workspace large? How many projects do you have in the workspace?
Can you try some steps for me?
1) Export all your projects. Start MyEclipse with -clean option for the same workspace. Now import all the projects to the workspace. Check if the issue persists.
2) Since preferences are persisted on a workspace basis within MyEclipse, you have to export your workspace preferences and import them to your desired workspaces (File > Export > Preferences)
3) Have a look at these threads and try the solutions for MyEclipse :
http://stackoverflow.com/questions/207843/how-do-i-prevent-eclipse-from-hanging-on-startup
http://eclipse.dzone.com/news/create-new-eclipse-workspace-w
http://stackoverflow.com/questions/881655/importing-exporting-project-preferences
Let me know how this works for you.