The problem could be traced back to a ROOT problem. Meanwhile the bug in ROOT was fixed and the memory leak vanished.
The patched versions are already installed at GSI, so if you use any version installed at /misc/cbmsoft you will have no problems.
If you use your own installation of FairRoot you have to follow the description below to update your installation to the latest patch.
After this steps you will have a patched installation of ROOT and the memory problem should be gone.