Thanks for the log file. It looks to me that something is fishy when upgrading your old 2.x workspace to 3.x. You can try the following things to fix:

1. restart with the -clean option (run STS from the command line and include the -clean flag)
2. delete the .metadata folder in your workspace folder and restart. You will need to re-import all the old projects. (actually, don't delete, just move the .metadata folder to somewhere else in case you want it for some reasons). If you have tweaked your settings, and want to save them, you can go file -> export -> settings and then re-import them after creating the new workspace.

Apologies, I'm on vacation right now, so don't have much access to email.