PokerTracker

I've installed PT4 and IGC on a new computer, as usual, I've proceed to opne a table up and position the tabs accordingly but when a player leaves or the number or the players changes from 6 to whatever other number, the HUD is scrambled again.
I haven't happened to me before so I don't know whether there's some new config or setting that I'm not aware of

Have you set different HUD Profiles based on the number of players? If a different HUD Profile gets loaded when the number of players change then that HUD profile is not going to use the same HUD positions so you'll need to adjust and save the positions in that HUD Profile too:

Guide: HUD Options & Profiles (Profile Select)