Thats usually down to the plane having a slightly different alt hold setting on its autopilot
like having to set alt then arm it which the logitech panel cant do . usually once its armed panel will show correct alt, what this means is you cant use the panel to set the alt but usually works for everything else. Planes i know this affects is BAe 146, concorde, Carenado PC12, Emb 110 and i think 787 and pmdg 737 to me its not a huge deal i set alt on the cockpit panel then use VS on the logitech panel ok