I have my wonderful Galor all set up nicely in the 3 bars so all my BO skills are where i need them, now i swap to my Freighter to do my Doffing and a little while later when i swap back most of my skills are no longer there and have to be manually put back

Is this a new thing as im sure it did not used to be like that as doing some of the missions where you have to swap to a shuttle would get really annoying

I thought it always did that. Every time you switch ships, it messes up your BOffs.

No, this is fairly recent. I was able to swap between cruisers, escorts, sci, whatever and not have my powers go all screwy on me, but recently they're messing up every time.

It would be handy to be able to save your skill bar layout. Better would be if the game remembers your skill layout automatically.