To be more specific, if a BOFF has been assigned to a station on one ship, and you change to another ship and assign them to a station on that one, the station they had on the previous ship will no longer be assigned to anyone. This can be very irritating if you use the same BOFFs on many different ships (and I know most people do).
Thankfully this doesn't affect the position of BOFF abilities on the action bar, but it's still annoying to always have to redo the station assignments every time you change to another ship, especially if you're used to not having to do this. Devs, some people like to set-it and forget-it, ya know?
It would be nice if we could at least get an acknowledgement about this issue from someone in a position to do something about this.