Using 1.2.2.

The Auto Enchantment Table will drain the XP accordingly but it will only enchant the item if you drag the slider to a number between 1 and 8, 9 through 30 have no effect no matter the level of the EXP that the Auto Enchantment Table contains.

I just had the same problem but I figured it out, it really doesn't like having drains or other blocks on the ground next to it. It doesn't "see" the book cases when the drains are down there. I hope this is fixed some time in the future.

Keep the drains outside the bookcase area :)
You can still put the tanks under. The drains are made of iron, this iron lowers the intensity of the EMF field from the magical enchantment table.. causing it to be less effective, or some other sci-fi excuse :P

Have you surrounded the Enchantment Table with Bookcases?
It still works the same as a normal Enchantment Table, only that it's automated.