To solve your situation without quite being able to explain it, if you go to the main Musicbee dropdown in the top left, Tools, Tagging Tools, Renumber Tracks, you can number the whole lot in one hit, including with multiple discs or albums. You can also set up a hotkey for that to speed things up.
At a guess, if you think of unnumbered tracks as being 0, when you do number one of them the order would become 0001 and send it to them bottom, now being the largest. And at an even wilder guess, does the tag editor think you're 'forwarding' from position 1 to position 2, then 2 to 3, with no regard for actual tags? When I have edited some tracks manually, I find working backwards is a bit more reliable, as you're moving backwards into the 'static' order you have before. It does seem a bit bizarre sometimes I agree, but it should only have to be done once.