My suggestion is try a NVidia card.
I've got both cards working now but the "solution" required some very backwards-thinking.
I moved the LSI 3041e into the x16 slot and the Radeon 5450 into the x4 open slot. I won't be doing any serious gaming so bottle-necking the video card to x4 shouldn't be an issue. Both cards (and the gigabit nic in x1) get detected and are working properly.
You made a right choice.
Radeon 5450 performs equally "well" even if be plugged in a x1 slot as it is in x16, this card even can't beat Intel HD4000.