I had this problem after installing the latest eclipse and installing subclipse from the marketplace. To resolve you can follow these steps:
- Click Help >> Install New Software…
- Set Work with:
Subclipse 1.10.x Update Site - http://subclipse.tigris.org/update_1.10.x - Ensure Hide items that are already installed is checked.
- Click Select All.
- Click Next.
- Complete the remainder of the installation as usual.