I found out that the batman-exp daemon goes crazy when its internal life-time variable overflows. This will happen after 49 days, 17 hours, 2 minutes, and 48 seconds (which corresponds to 2^32 milliseconds). Unfortunately, its behavior afterwards can be anything between hanging around and doing nothing and an endless loop of sending packets. The problem is fixed with revision 972.
If you are running batman-exp I strongly suggest to update.