Hmm, just a suspicion, but in TS go into edit mode and see what happens if you grab some of those problem verticies and move them away from the rest. They should drag all their connected faces with them - do they?
If they do drag the faces with them, it means it's just PCS not being good with the smoothing rather than disconnected faces.
So, in this case I'd recommend you try with a standard build of PCS. This time you'd set the rest of the ship to faceted, and the gun pod to auto-faceted (angle doesn't matter). This should result in a faceted ship and a smoothed gunpod because of TS being mixed up in smoothing types.

Failing all that, just subdivide the rings at either end of the gunpod and move the new verts around to make it smooth geometrically.