I was on the phone yesterday to the OnePass Service Center concerning missing milage credit. I was told that the computers will not post credit for any flights on a reservation record if a ticketed segment is missing (in my case I was rerouted for one segment on another carrier) I was told that in this case I had to send in the documentation that I had completed the entire itinerary in order to receive credit.

For what it's worth, I inquired about the 2000 elite program and was told that it would be basically the same, except for some "enhancements" to upgrade opportunities for lower level elites.