I have two non-hiding expanded panels on the top of my screen (Panel A
'under' Panel B). I order them in such a way so that a specific one is on
top. If I ogout then in, they always come back to position B 'under' A
(i.e. they dont swap if I logout with B 'under' A).

I am not sure how this can be reproduced. A good way might be to try and
create simmilar panels, and if after a reloging they dont swap, then swap
them manually and then relogin.