Sorry for the late reply.
> Should I open an issue in JIRA?
Probably. It is possibly a bug in STS gradle support.
Since there are a bunch of different ways to create / import projects into STS (e.g. many options in the import wizard), it is important to provide some very precise instructions on how to reproduce the problem. Ideally, provide a small sample project and exact step-by-step instructions on how to get this project into the workspace so that the problem happens.
If you think you are able and willing to provide this amount of detail... Please *do* raise a Jira issue and I will be happy to track down the origin of the problem and fix it if is is indeed an STS problem.
Kris De Volder -- SpringSource