I'm not sure what the problem is. I have not seen it before. But I think it is some problem within how the Gradle tooling API connects to the daemon. I.e. I think the problem is on the Gradle side, not the STS side. A good place to try and get help with this is the Gradle forum. What you are seeing could in fact be a bug in Gradle tooling API and infrastructure.
The gradle forum is here.
It is possible that you can 'fix' the problem by adding arguments to the gradle operations. In the 3.0.0.M2 version of Gradle tooling it is now possible to add extra arguments in a global preferences page. So, if the gradle guys have an idea on what may be causing the problem connecting to the daemon and suggest adding some commandline options you'll need 3.0.0.M2 version of the tooling.
Unfortunately, these are not compatible with STS 2.9.x... but I can help you get this setup if need be. Just come back here with questions about that :-)
Sorry I couldn't be more help.
Kris De Volder -- SpringSource