sry, but my BOFF setup stays exactly the same when i switch ship...if it was a ship that i previously already set up. A new ship will allways be empty.

if i switch between my 2 escorts, everything is in place on my second escort. When i switch back to my first all boffs are setup and ready to go, so are all boff powers in the tray of both ships...allways.

the only stuff that gets inbetween are weapons on the tray...i remove them manually, or put them soemwhere in the 10th row.

not sure why it is not functioning for you, for me it does.