Looks like you're right.
Testing a few times now it looks like the workflow I described will always produce a bad trim on the first try. *However* Hitting CTRL-Z and then redoing the trim always seems to fix the problem. I've done this 4-5 times with different files now.

1: turn on snap to grid.
2: draw a dome-like curve
3: extrude it
4: create an arc for trimming the corners (Like in the file I supplied earlier)
5: do a trim of the extruded object with the ark

You now have an object with a malformed trim at the corner(s)

6: Hit CTRL-Z
7: Redo trim (Not CTRL-Y)

You now have an object with a good trim at the corner(s)

(Edit: looks like we both found a workaround at the same time:-)