Thanks for your help, I really appreciate it.
So, as a first pass I will add the derive_clock_uncertainty clause to my sdc file. At leat I will then know if I'm way out.
The lower end of my setup slack distribution curve is quite low (100pS or thereabouts), so yes I could try setting a minium slack constraint. I'm not so sure what margin I should use though, until now I have assumed that any value of positive slack is OK given that I'm checking all 3 v-t points.
I do take the point about SignaTap. I do use it when I hit problems and it has proven to be extremely useful.