I expect you have already checked that the liner protrusion is fairly even around each individual liner by measuring each liner in at least 4 places (after trial assembly and torque up with an old gasket)
Apparently it sometimes happens that the block around the studs can become raised if the head has been over torqued or if the studs were not seated deeply enough in the holes. Is the block itself perfectly flat?
You could also try the TR Register forum and search 'liner protrusion' or similar
