OK, so I was wrong. It turned out to be a rendering problem after all, and the pre-converted maps only worked because the conversion script just happened to accidentally work around the bug.
Unfortunately, I can't even blame the QT upgrade tool... Due to API changes, I had to rewrite some of the line drawing logic in order for it to work with QT4, and in the process I managed to screw it up. So it's totally my fault. Sorry about that.
Anyway, as far as I can tell, it's fixed now. I've tested it with a handful of random maps from SOE, Brewall, and Good, and they look normal to me.
Though, there could still be lurking issues with the rendering changes, so if anyone *does* want to do a bunch of map testing, please go right ahead.
I've committed version -pre5 with the fix.