Hmm, ok, found something else out that clues me in to something here.
I knew if I restored the text-indent, popup menus came back. I wanted to see if shifting them over 100px was moving my "click detection" area over also. Turns out it doesn’t move the hit detection hotspot of the menu, however my actual popup menus were shifted 100px to the left. This explains why my popup menus aren’t displaying. They actually are, but -9999em offscreen.
So now I need to find out how to get the popup menu shifted back into the right position, with the parent li text shifted left offscreen.