Use of eclipse classpath variables for jar dependencies?

In a project that uses my local maven repository for jar dependencies, I have
the dependencies defined using the standard M2_REPO eclipse classpath
variable. When compiling I get an exception in scalac (see trac issue
http://lampsvn.epfl.ch/trac/scala/ticket/1918). Miles closed this issue as
"works for me".

Does anybody have any idea what I might be doing wrong? My M2_REPO based
dependencies are indeed pointing the jars that exists. The M2_REPO variable
is indeed configured correctly in eclipse to point at the ./m2/repository
directory. When changed the project to use external dependencies pointing
directly to the fully qualified path everything compiles fine.

Is anybody else using eclipse classpath variables in their projects?