When a project is imported using the "Import >> Existing Projects" wizard, and we do not select "copy project into workspace" then if you try to deploy the project with "run on server" context menu or by drag-drop to Tc Server, it will not work.
The reason appears to be an issue with the module cache which is being created after the project appears in the workspace. With linked projects the project appears first as an "empty" project and then in second stage the project contents appears.
WTP will ask for the modules as soon as the project appears, but since it is empty it will not look like a grails project and not have any modules that can be deployed. This result is cached. The cache isn't cleared once the contents of the project appears.
I've got a fix already and will commit shortly. The fix will be in 2.5.3 (or whatever is the next release after 2.5.2.
Workaround for 2.5.2: restart STS.