With Eclipse Mars and BuildShip, I then used Eclipse > File > Import > Gradle Project. I checked out the entire project source with Eclipse then deleted the temp project (needed to Checkout via SVN) and. No one was running BuildShip so I thought I would give it a try (works great other than this issue so thank you!!!).
I recently joined a new team that uses Gradle. On each system I have a large Java project which does not use Gradle and existed long before creating a new project that lives in a separate workspace that uses Gradle. The only other plugin installed beyond Gradle Buildship is SubEclipse used for SVN.
My PCs run Windows 7 Enterprise 圆4 with Eclipse Mars 4.5 64 bit (Eclise IDE for Java EE Developers), Java 8u51 圆4 on one PC and Java 8u60 圆4 on the other, Gradle 2.7, and Buildship Eclipse 1.0.3.v20150917-1110. I can easily reproduce this problem on 2 separate PC systems with the exact same configuration.
