Sorry, hit the create button too soon. In the following more detailed description.
I'm using the maven-bundle-plugin together with the maven-jar-plugin (to create OSGi meta data for the MANIFEST.MF(_maven-bundle-plugin) file). In short, the bundle plugin creates a MANIFEST.MF file containing all OSGi related meta data. This file is taken and merged by the jar plugin into the final MANIFEST.MF file (note that the documentation http://maven.apache.org/shared/maven-archiver/examples/manifestFile.html states "The content of your own manifest file will be merged with the entries generated by Maven Archiver.").
The problem is that the "Class-Path" property gets lost although configuration of the jar plugin is set to create it, see MANIFEST.MF_final_with_maven-bundle-plugin. When the build runs without the bundle plugin (by deactivating corresponding lines in the POM) the "Class-Path" property exists, see MANIFEST.MF_final_without_maven-bundle-plugin. This makes me believing that there is a bug in either the jar or the archiver plugin.