After much frustration I think I worked out what the problem is/was. When I last got disconnected with a server crash, I was in a mission where I took on a disguise and the abilities of one of the NPC factions. It seems that when I logged in next, although I no longer had the disguise or abilities, the tray was still locked to the faction abilities. I ran the mission again to complete it and upon exiting, my trays were back to normal.