I guess my concern is that ever since we truncated the sys_datalog table to clear the jobs that were simply stacking up we found the jobs queue stopped being added to (apologies if this was not clear from my earlier email).
Ok, then its clear what the problem is, you should have mentioned that in the first post! Never delete records manually in the sys_datalog or you will break the system! The jobs in sys_datalog are cleared automatically by ispconfig, so do not touch this table.
If you truncate the table, then you reset the auto incremenet ID's of the table which causes the server jobs to get out of sync.
To fix the problem, edit the server record in the server table and set the value of the updated column to 1.