You answered your own question. DI sucks. I disable the direct out on my amps so they can't use it. When they ask me to plug into a direct box right off the bass I refuse. You can't get your tone out of anything but the cabinet being mic'd.
dont spew in this age old argument of DI sucks and MIC is better. this just proves that you are stubborn and so far stuck up your ass that you refuse to work with people who can actually do their job. im sorry but this argument really pisses me off...(can you tell)
everyone has their own sound and own feel of what they like, personally i prefer to use MY SANSAMP which has a balanced XLR out, which i could argue to you is better than your crappy micing the bass amp. and we will get no where...this way i know that if my amp craps out that i have great tone going to FOH and then i can use whatever amp i want and get great tone going there and adjust to the characteristic of each amp. your statement is a false representation of reality.
that being said...as jaywa said it could be a phasing issue too. i never thought of that...