Interesting. In retrospect, I may be suffering from a slightly different issue, because tweaking the Default Font Line Height fixes the vertical alignment of my fonts, but I can't find a way to fix their horizontal positioning.
I do wonder what changed between GlyphDesigner 1.5.8 and later versions, though. That was the version I used when I originally imported my fonts months ago without any headaches. I needed to update a few of them today, and that's when I found everything misaligned and whatnot. After trying a bunch of different things, I reverted to the version of GlyphDesigner I had been using when I did the original problem-free import, and it worked like a charm.