All right, after some wrestling, I installed the new FairRoot release, this time with ROOT 5, as ROOT 6 wasn't really working out for me. However, I still get the same warning from the timebased digitisation macro:
-E- FairMultiLinkedData_Interface::AddInterfaceData EntryNr == (-1/-1/-1/-1/1)
I first reran the simulation macro as well to be sure everything was done using the new FairRoot.