Something has changed, as this didn't used to happen:

I have Targeting Extension at level 3 which lets me have 4 locked targets. However, my Termis only allows for 3. So with 3 targets locked, I find that if I click (left or right click) on either the second or third target in my Targeting Computer window, that the second and third targets usually switch positions in that window.

In the recent past, the targets used to populate that window in the order that they were locked, and they would stay put.