When you import a Gradle multi-project and check the option to create resource filters for subprojects, it seems like those resource filters are not applied correctly under Windows.
Suppose you have
and that mainproject is located in D:\mainproject
When you import in Eclipse using the Gradle Import Wizard, on mainproject the following resource filters are applied:
Project Realtive Path equals D:subprj1
Project Realtive Path equals D:subprj2
while they should be:
Project Realtive Path equals subprj1
Project Realtive Path equals subprj2
The result is that the resource filters are not working, and I see the subprj1 and subprj2 folders in my mainproject project in the Eclipse workspace (either in the Project Explorer or in the Package Explorer).
A co-worker of mine, which is working with Linux, does not have this problem.