Well in fact, I didn't exactly fix the problem.
As it turns out, Targas have a flag in their header telling you if they are top to bottom or bottom to top, and I didn't know that, so I used to always flip. That obviously failed.
Then I tried moving the call to the flipping function in the non-RLA 32 bits per pixel targa case, and that seemed to fix it for the files I was testing with, so I thought "Hey, that fixed it".
Anyways, I gave Darky yet another version today, and this one will really work for all cases, since I went back to the targa specs and realized the existence of the top to bottom flag.
As an aside, I don't support right to left targas (that's also a flag), but rarely anyone uses that, so that should not be an issue. In fact, most of the smaller editors tend to ignore that one. Perhaps when I feel like it I'll add support for that one.
Since we're into limitations, I don't support paletted targas, 16 bits truecolor targas and black and white targas.