Thanks Graham for the compliment!
Thanks Klaas for the suggestion I've just got back and had a quick look into this. However I don't think it is EHT regulation as this happens with or without flyback suppression and doesn't vary with picture content. (I tried a pure grey raster with all lines the same and it stayed like this.)
Next I tried disabling the V & H outputs and looking at the line drive waveform (to rule out feedback / decoupling issues) and there is still a problem. Watching the line sawtooth from the buffer after the 555 it wobbles at about 12.5Hz with all other circuits out (i.e. just clamp/sync seperator and H sawtooth and flywheel sync in place)
I can actually see a very small variation of the flywheel sync control voltage (just above the noise floor of my scope). This I think may be the "missing" control update during the missing sync line - I've used a double diode push/pull phase detector but this must be leaking during the flyback and causing a ripple? However this could be a symptom rather than a cause!
I'll try and have a look later tonight but I've just got back after a long and frustrating car journey (long in time not distance!) and need a cup of tea and a lie down!
Thanks
Dom