The info I could find seems to suggest that it was the original title but I couldn't see anything to suggest that it was released with that title, ie it was Thunder Bolt in production but Death Proof for release. It was left in to match the way it's filmed -

Quote:
Death Proof uses various unconventional techniques to make the film appear more like those that were shown in grindhouse theaters in the 1970s. Throughout the feature, the film was intentionally damaged to make it look like many of the exploitation films of the 1970s which were generally shipped around from theater to theater and usually ended up in bad shape. A notable example of one of the film's deliberate jump-cuts is seen at the beginning, when the title Quentin Tarantino's Thunderbolt is shown for a split second before abruptly being replaced by an insert with the title Death Proof, appearing in white lettering on a black background.

Oh, and I thought it might have been something more mysterious, or at least license problems with one of these titles.

Yeah, it's simply a cultural reference to the age-old trick of taking a film and splicing a different title into it so it could be marketed as a "new" film.

If you see this happen in an older explotation flick, it probably is the real title.
Here it was just another gag to give that old explotation feel. Ironic that the old flicks this os done cheaply and by accident, where here it was probably expensive and mapped out to the frame.