Do you use the Mic and Cab emulations in your BOD? If so, turn them off or try new ones. Those emulations often lead to boominess when used for recording. Especially with some of the default patches in the BOD Live. I spend a lot of time tweaking my BOD to get the sounds I like when recording, but once you figure some of that out, you can get some fantastic recorded tones out of it.
Another question that comes to mind is, are you using the DI out or the Model out for your recording? The DI is a dry signal and doesn't carry the modeled sound. An undocumented feature of the BOD is if you plug something into the Headphone Jack, you'll get the modeled sound through the DI.
Best of luck!
