I don't think I've seen any actual plot holes yet. Really, carefully thought out and consistent time travel mechanics are more or less indistinguishable from asspullery. What seems to be taking place here is that Hussie is just winging it, writing mechanics as he needs them, but keeping things ambiguous enough that nothing is explicitly contradictory.
Regarding the infinite Dave cheat: Yeah, saying that creating offshoot timelines only works SOMETIMES pretty much conclusively fixes everything.
I figured that it couldn't be the regular old multiple-worlds thing with no twists whatsoever, since there is canonically only one timeline that isn't doomed; but making it only branch out at certain points explains all the observed phenomena, and is perfectly consistent with the mindfuckery that is Sburb design. No reason in just dropping a command capsule in a meteor, if you can drop a command capsule in like a hundred meteor shards that end up sprinkled all over the world with a special mechanism that's housed on a different meteor (that landed hundreds of millions of years ago on the same spot the exploded meteor was headed) that can pull them all together again if you use a special key on it, a special key that apparently only the Queen of Prospit has.
Re: Armok's question:
What the hell are those railmen doing on the rails, anyway? I don't see how it would be my fault if they get squished if they make a business of standing on railroad tracks.