I find a big difference between mucking around with it at home or getting it out for a quick fiddle when flying, versus mounting it on the windscreen and using it as it was intended and letting it do its' thing over a longer flight. Both apps seem to get a little confused sometimes particularly if switching between screens and rushing things, but much better on the iPad 2 and crashing is far more un-likely.
One chap at my airport was complaining about Ozrunways saying it was crashing and doing silly things, however once I saw him using it I noticed he was doing silly things, like accidentally clicking on the scratch pad, accidentally clicking on flight plans etc. Not saying that's what you're doing but it reinforces my point of letting it be and doing its' thing.
One thing that also tends to happen is you accidentally click on things if you are manually handling the iPad versus having it mounted on the windscreen or kneeboard.