Just a follow-up - I sent the support team a set of seven subs (in fits format) which I took a couple of nights ago. The second sub stacked with the base first sub, but the next five all produced the infamous "Cannot find matched triangle" error, and all subs had tight stars. The response I got from support was they could not reproduce the problem, and they suggested I try another computer.
If they can't recognize this problem, I'll revert back to vsn 1.1 which I believe had robust livestacking, or stick to SharpCap which has no problems of this sort. A bit of a disappointment to be honest.