I guess I tried to oversimplify my problem by using the 2 intersecting pipes as an example.
The vertical pipe was actually formed by rotating an elongated box while the oblique pipe was constructed by sweep (or rail sweep, not sure since one works with shelling while the other doesn't. Don't understand why).
I can reproduce your example, but when I use a rotated box, I get similar results to my original problem. (I have to say that TC17.2 does act quirky when I do sweeps or rail sweeps!)
Haven't tried your approach yet, but will shortly.
Thanks to all for the responses thus far.