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It seems that I have found the problem. Maybe the following solution will help someone else who also encounters this problem:
Ultimaker does not use pure Marlin as firmware in the UM3, but a slightly adapted version of it (Griffin). This one does not support the commands used by the extension M82/M83 (Relative vs. Absolute Extrusion) - at least not without errors. You can read this in the community post of a former software developer of Ultimaker about the release of the UM3.
Sometimes the code was executed correctly, sometimes not. When it didn't, the command was implemented with the E3 extrusion absolute and not relative, so as the layer count increased, the filament was retracted further and further, only to be fully retracted again with the next extrusion command. I modified the Cura PlugIn so that the retraction commands are inserted absolutely in the code.
