For some reason, my auto populates it self at will lol.
Like, The "Devices" on my ship, I could never get them on my bar. And I had other skills in the spots. And then one day I login and the two devices are in there. heh.
But ya, I thought it was mainly due to lag, but I'm not sure. Even when you put weapons on or off, or take them from your inventory and put them in your bank, it seems to take a good 10-20 seconds for it to happen. The boxes will stay lit up. So maybe it's the same problem with the hotbar?