Fixed it. Had to uninstall the AJDT and the Spring Ide AJDT, and then update both Spring IDE AJDT and AJDT (via marketplace) and everything is working properly. This may have been an issue from the Indigo->Juno upgrade I did within Eclipse.
Hopefully this can help someone else in the future. One thing to note, the Spring IDE update site has changed for Juno to http://dist.springsource.com/release/TOOLS/update/e4.2/