Did you pump items out through the top, and in through any of the other sides? If not, there's your problem.
What are your requirements other than "must store output items in its own inventory"?
You could also try the Liquicrafter from Minefactory Reloaded (which crafts once upon receiving a redstone pulse- so you'll need a timer of some sort), or the Cyclic Assembler from Thermal Expansion (which probably has the advantage that it can auto-eject items if needed; but I still don't know how it works).
[Edit] Darn, ninja'd... [/edit]
There's also Factorization's autocrafting chain, although there's probably a reason that it's not used often. For one, it eats paper; second, you need a different block for each different material and another to actually make the item. It is, however, the only technology I know of that can create a universal autocrafting system- although I don't know how you could do it without a Redpower Sortron or a bunch of CC computers with Interactive Sorters linked together.
