The question on why Apollo's rank changed back to Major is that after the Pegasus where he held the position Commander (of the Battle Star) which is a position filled by someone with the rank of Commander was destroyed he returned to the Galactica where he held the CAG (Commander of Air Group) position which is a position with someone of the lower rank of Captain or Major.
In the episode Exodus part 2, in one of the deleted scenes on the DVD it shows the discussion between Admiral Adama and Commander Adama in the CIC (ship command center) discussing what is needed next and the Admiral says the highest priority is to get the pilots & their fighters who protect the fleet back up to standards because they had been away for years while trapped on New Caprica by the Cylons and they need Apollo as "the new old CAG". Apollo agrees and jokes that the book (regulations) says that CAG is a position for a Captain or Major so that means he will have to take a demotion pay cut which would cut his retirement pension plans ;-). Adama stayed an Admiral even with only 1 ship left just like Admiral Cain when she only had Battle Star Pegasus left.
Fact that Apollo had Commander rank insignia means had he had the rank of Commander. Just like in the U.S. Navy anyone who captains / commands a ship is addressed as Captain (position) regardless of rank. Being ship captain does not mean you can put on the Captain rank insignia. FYI: a Mark VI Patrol Boat (descendent of the PT Boat) is commanded / captained by a Lieutenant.
Also the CAG as a department head reports to the Executive Officer (XO) who is second in command. Commander outranks Colonel (i.e. Commander Adama and Colonel Tigh) so as a matter of chain of command it was most expedient to simply reduce Commander Apollo's rank back to Major rather than have him routinely reporting to and answering to a lowering ranking officer Colonel Tigh, XO who has higher position. Everybody gets their old job back. Career paths are limited anyway in a one ship fleet when you are in the top echelon & pay difference doesn't seem to matter as much when you are trying to survive for another day as a species.