Yeah he seems to be getting a bit better these days. It definitely made him uncomfortable but that's necessary for growth I figure. He made me uncomfortable too, his Pluto and Saturn in my 12th (Saturn really near my ascendant though).I think the thing is it helps him to face up to his stuff and be loved anyway it's not like other relationships didn't bring these things out in him but I'm actually able to withstand it and nurture his goodness from a philosophical standpoint
then again Jupiter definitely has a dark side and it is in over enthusiasm and expansiveness and that certainly has played in also.
I would look to other chart factors to understand the dynamics between you. There are other things which would be likely to make you uncomfortable. But the propensity to exaggerate or over emphasize your unconscious could easily make you uncomfortable.