[Darryl Ramm]

What are you doing? What is going on between the earlier and later part of the recording when it cleans up.

Did you solve the output unbalanced issue?

As said before: we cannot guess what you are doing: You need to try to describe what you are doing. What guitar, what exact pickups? (to try to explain the high frequency flanging effect) Are you monitoring loud enough that the signal may be feeding back through the guitar? (if so try tracking with headphones). What exactly is in the Eleven Rack rig? Start with a amp only and no rig or external effects pedals. What exactly is connected. This is the wet recoding into you DAW straight from the Eleven Rack or miced from a cab or ???

Confirm that on cleaner settings cranked up you are not hearing any strangeness, anything intermittent with the guitar or pickup, or RF/noise pickup on the Eleven Rack... obviously that will be higher with high-gain amps. And there may be a lot more chance of pickup with the Eleven Rack that an amp, because you have more possible ground loops with computer and USB cables etc. I'm not confident of this (I want to know exactly what your setup looks like), and are not looking for "hum" but more high frequency "hash", so get a decent clean amp only rig, turn up the gain and play (guitar location, orientation, how you are touching it etc., computer connected or not, external monitors connected or not, etc. around looking for noise that may be causing problems.