When I've felt such feelings, it seemed to stem from a knowledge of just how filthy and philandering men can be (due to being one).
Woman-on-woman action involving my partner felt less threatening both because the idea of it was (true to the stereotype) exciting to me, and because I had some vestigial feeling that the act itself was somehow less primal, raw, and fraught with risks.
The final point is true, to a certain extent. STD transfer rates are FAR higher in M-F pairings than F-F, and there's always that pregnancy issue lurking. That's not the core issue, though.
Conversely, at this point, as one of the wings in an MFM albatross, I find myself with zero apprehension about it. I can sit there and think at length about my girl and her boy together, and feel nothing but perhaps a little arousal. I think these feelings are very situational, and they can be bested, if it's worth it, with some work on yourself. They don't have to persist.
In this case, the matter seems to be helped by the fact that I know, regularly converse with, and see the other guy. I know he's a solid person and won't treat my girl badly. If it were someone I didn't know or knew but disliked, I think things would be different and I'd be experiencing that same pit-of-stomach discomfort you speak of.