M6 the last 74LS161 in the vector timer chain was dead. Never doing anything, as a result the !Stop line was never going low. As a result the AVG was still waiting for the Center to complete.
I had looked around there before but was thinking that CNTR was counter.
I need to try to write up a doc on all the signal names and uses.
Oh and while I have the AVG fixed the board is still broken, no X deflection coming out of the vector generator.
One problem at a time :)
Thanks loads for the help Jess.
David