it's probably happening during obj export rather than in 3d coat. That's the usual cause on our zbrush/Maya disasters check your export settings in both apps for anything that might do it.
Just to update anyone with the same problem, after a few tests I think poopipe was right - I switched all the OBJ export settings from Maya (Groups, Materials, Smoothing) to Off and when importing back from 3D Coat didn't get any seams in the UV. Still have to see if I get problems later as it could just be a 'one off' but…