I hate doing this, because I (like most of you) don't know enough about philosophy to comment, but anyway...
Any proof of God can be refuted. God is known to be unknown, so any given proof is nothing but a test of faith (or lack of faith).
Here's a step by step recap of looseBits' post:
1. Definition: A god is that which nothing greater can be thought.
First of all, this sets the word "God" to Boethius' interpretation of God. If you talk about flaw, talk about it here, in Step 1. Boethius attempts to define God, therefore lowering God to the level of a definition. A definition is a framework that bounds an object or idea to other objects or ideas, so in effect Boethius tells you from step 1 what God IS and what God IS NOT. To most, I'd say that's an insult. But for a second, say you've defined God in the same way as he. Then comes:
2. Assumption: It is greater to exist in reality than the mind alone.
Here looseBits misreads the actual assumption. He separates Reality from Imagination, and views them as two separate worlds. The proof, however, implies that anything real can be imagined. To elaborate, the assumption can be broken down and restated as follows: (1) Imagination is a vast world in which anything can exist. (2) For the sake of this proof, let's assume there is a certain greatness involved in being Real and (3) that Imaginary greatness is complimentary to Real greatness. Then the greatest thing imagined is complemented by additional greatness IF it is Real. It is greater to exist in both worlds (real and imagined) than in the mind alone. If you think that's good enough, then:
3. QED: A god exists.
Then again, maybe he doesn't. All those hidden assumptions have to be made as well, collectively undermining the validity of the proof.
What I discussed above has nothing to do with the existence of God. It merely deals with my personal ideology.
Boethius' argument is ontological. There are multiple ways of disproving it. For example, Emmanuel Kant and Bertrand Russell's argument against this proof is that existence is not a predicate. Existence is not a quantifiably greater attribute than non-existence.