Just following up. Unfortunately the LCELL did not fix the problem.
But it seems that the flip-flops not being put on the global clock line were hidden in a partition with the automatically set 'post-fit' type. I moved them to 'Source File' (always gets re-synthesized) and now everything is happily on the global buffers.
Sometimes I wonder if the 'make' like features of SW might actually cost more time than they save!
I did find, buried in the fitter info messages, that it mentioned it was not connecting these flip-flops to the global clock. I would have been nice to give this as a critical warning especially as I had purposely assigned them...
++Simon