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I've noticed several times after checking all my projects out from CVS into a clean workspace that afterward several don't build. They are ones that depend on jars from plug-ins (usually JUNIT). These are in the project's build path as extensions of the ECLIPSE_HOME variable. They are failing because for some reason ECLIPSE_HOME is not set! The problem goes away if I exit an restart Eclipse. I can then get the projects to build. I'm not sure if CVS is involved, but that is when I see it. I haven't tried to see if it was unset before.
This is a duplicate of bug 20197. A combination of several issues where involved in this bug. Fixes are available in 2.1 stream.
*** This bug has been marked as a duplicate of 20197 ***