According to the Release notes for Feb. 2 2012 the Consoles should have stayed in the Eng. Slots... But once you beamed to Ship or did a Mission, they where Automatilcaly moved to the Overflow Bag in the Inventory Window.
Engineering Shield HP and Shield Regeneration consoles are now Science consoles.
If you have one of these slotted in an Engineering console slot, it will remain there, but if you move it, it will only go back into a Science Console.