How did you plug the guitar directly into the the AR2412?
With the direct box are you using both inputs at the same time with the guitar source
inputs?
Are you using standard tip/sleeve 1/4 cables to plug in to the direct box?
Maybe it’s phase cancellation from combining the two input sources. That could be from
one mis wired XLR cable or the phase/polarity button being turned on on one of the channels.
You CD with split tracks since the input sources were different would not really
show that kind of issue.