I've never used the auto anvil before, so apologies if I mucked this up. I'm using 1.3-snapshot 513 in the Direwolf20 1.0.3 pack.

I built an Auto Anvil, dumped 60000mB (!!! Apparently you can't get this back out?! And apparently it'll suck it in as fast as it can before I react? Crap!) of LiquidXP in, then (manually) dropped damaged diamond pants and a diamond in.

It partially repaired the pants just like it should.

Then I put diamond boots and a diamond in.

It repaired the boots, overwriting and deleting the partially repaired pants that were still sitting in the right-most slot.