I downloaded the same firmware files again, removed everything from the flash drive, copied these fresh files to the flash drive, verified with WinMerge that they weren't corrupted, then updated the firmware on the scope again. Now it's the correct orientation and has stayed that way through a couple restarts. So maybe file corruption, or some weird setting (like RTL layout?) that carried over from the old stock firmware that's now overwritten.
Edit: Darn, it mirrored itself again after running for a while. Very odd, maybe a hardware issue with the display?