That's an interesting one - VLSI! This may be the cause of the whole trouble, as the phase shift of the output Pixel clock of this Lisa may be totally different than the three other versions that I know of.
I need to dig through my stock of A1200 boards to see if I even have one of these. It might enable us to reproduce the problem and find a fix.
If you could do noe more test and switch off the PCLK pull-up resistor? That should at least change the behaviour.