Hi,
the fact the timetable seems to be 'messed up' is because we decided to create a more realistic one.
This also involves that planes start/arrive only from/to hubs. In the 'old' timetable, we just introduced flights no matter where the huba and planes were. Now every plane has it's individual schedule; for example, for every flight starting at EGNM, a plane has to fly to EGNM first, from EGLL (or some other hub).
On a similar note, if LKPR-LKTB was operated by a Class 2 plane, we'd first need to get a Class 2 plane to LKPR, from Zurich, Amsterdam or Stockholm to fly that flight, and it wouldn't be quite economical. As there's already a Class 5 plane that does the ESSA-LKPR flight, we just make another stop in its itinerary, to LKTB.
The system can be understood better if you download the Offline timetable and click on a flight number to see how is it exactly operated.