The errors in your log file seem pretty harmless. (The 'Fatal' error is some Eclipse/STS component trying to parse an empty .xml file somewhere, and it is being very vocal about this. The error is there all the time and not really an indication of a problem).
Unfortunately this leaves us with little info to diagnose a problem. The logs seems to say everything is ok. But what behavior you are describing seems to suggest that Gradle plugins are just not installed/active.
At this point I don't really have a good idea on what to do to diagnose it further. I'd recommend just trying to re-install the gradle plugins again, or is there a reason why you can't?
Kris De Volder -- SpringSource