Playing more with the price set I created in the sandbox. Sometimes the item gets moved to the correct place, sometimes to the wrong place and sometimes nothing gets moved. Moving the top one to the bottom or the bottom one to the top works okay.
Recreated this sequence:
Moving the fourth one to the top, then moving the new fourth one to the top will swap the old fourth one and the new fourth one, instead of moving the old one to second, the second to third and the third to fourth.
And this sequence:
Move the bottom one to the top. Swap first and second ones. Then swap second and third ones. The one you are moving jumps down to the bottom instead of third.
Hopes this helps track the issue down...