I figured out a way around it. Whenever I play through my amp and then run that into the interface, then into Amplitube (and bypass everything), the input volume is perfect. I know this is kind of a roundabout way to use it, and this doesn't allow me to use the gear in Amplitube (although I can use the pedals and the rack delay), but I'll keep troubleshooting the issue.

Thanks for the info.