The standard 2D tracker has a serious bug that has been there for many many years, from long before Blackmagic bought Eyeon. It's been reported many times with no response.
Basically the reference frame function is screwed - it can change the ref frame (and therefore the track) when you change the length of the animation, when you write out the comp file and read it back in and any number of other ways. It makes this function basically unusable.
The solution is to use Secondman's excellent TrackerPlus, available on Reactor and here
https://www.steakunderwater.com/wesuckl ... ipt#p10372which has a correctly functioning reference frame. Among other things it also allows single frame single supervised tracking, which is pretty difficult in the normal 2D tracking mode.
There have been many calls for an update to the 2D tracker over the years, again with nil response.