Steps taken:
1. Installed the plugin, added Clover to two projects: one containing a test, another one I wanted to measure the coverage for.
2. I've run a single JUnit test class with "Run With Clover | As JUnit"
3. The test ran fine, TestRunExplorer, CoverageExplorer, TestContributions were populated correctly.
4. But the Eclipse process in OS seemed to take more and more GDI objects (as reported by taskmgr.exe). This led to first Eclipse being not responsive, then even all the other applications having problems to render them correctly. The GDI objects number kept on growing until it reached 10000, which was enough for my computer.
Note that the GDI objects number keeps on rising without a single click in Eclipse after selecting the "CoverageExplorer" view (about new 8-12 GDI objects each second). Without EclipseForClover no such a problem is observed when running tests.
Reverting the changes in ".classpath" and ".project" and restarting Eclipse restores the proper behaviour.
Sorry, Michael, for not responding. I didn't get any e-mail notification.
Thanks for fixing!