Sadly I have experienced the ship shift issue. It’s very odd, it caught me off guard the first couple of times it happened. So far I have only run into it twice. I noticed when I really baby it though first gear it will let me go into second but if I run the gear out a little longer it will then lock it out. I have to admit that I have been getting on the car quite a bit so I will have to experiment a little with it and see when and where it actually starts locking out.
I've had 4 GM cars with the skip-shift (94 Z28, 00 Z28, 01 SS and 04 GTO) - all of them had a "skip-shift" light that came on when it was going to skip-shift. Does the Challenger have one? (I sincerely hope it does). If/when it comes on, all I had to do on the GM cars was to push in the clutch and goose the gas a little and it would cancel the skip. Also if you rev the engine a bit higher it would also cancel - try these in your Challenger and see if it works (it should). It only does it when the engine is at normal operating temperature, which is why it doesn't do it right away when the engine is cold - that throws alot of people. And of course if you're hauling arse it doesn't come on at all (or it had better not!)