Eclipse RCP features install but no plugins show up when i restart eclipse after the installation

Question

I wrote some plugins for an existing Eclipse/Equinox RCP Application. Previously i was able to install them just fine by using an update site.

After the RCP Application updated this is not possible anymore (org.osgi.framework.version from 1.5.0 to 1.6.0, osgi.framework.version from 3.6.1.R36x_v20100806 to 3.7.2.v20120110-1415):

• The features are installed (listed in features/, show up in Help->Software Updates->Manage Configuration).
• The Feature-Status shows No plug-in: "XY" included at runtime. for all plugins in the feature.
• The plugins/ folder contains the .jar files
• When i use ss on the OSGI console the bundles are not shown.
• The exact same update site works fine in the old version of the RCP Application
• When i install the same plugins from the OSGI console with the install command the plugins work fine. (Fresh version of the RCP Application/Using the same jars that were in the Update site)

What can i do to diagnose or solve this problem?

EDIT: If i press the Apply Changes Button instead of the Yes->Restart Button after installing the features they get installed properly...