Thanks for the JIRA. I fixed committed a fix for this issue.
I recently had this issue also in a new install of STS, with an import of an existing project.
In my previous workspace i had selected a custom roo install.
I checked my .settings folder, and i had the prefs file.
To resolve my issue, i had to right click the project and select the roo install i wanted in 'roo support'.
After a reboot of sts everything worked fine.