After doing a bit of research this is the procedure that seems to work to cure all aliasing, output, gain, noise, pop, clicks and other misc odd things. I believe the reason for this is extremely simple although CK will most assuredly need to verify. The problem is simply corrupted system settings and seems to occur out of the box. Simply upgrading firmware does not fix the corruption nor does deleting rigs.
The symptoms my Kemper was exhibiting was such:
1. Out of the box, first thing I noticed was poping/clicking every so often, I was using XLRs at the time. (I believe this indicates you have corruption)
1. SPDIF levels extremely loud, clipping on every preset into my audio interface, my SPDIF was set to slave to the Kemper and 44.1khz.
2. Sound was slightly odd sounding, never could put my finger on why
3. XLR outputs outputted a very gainy signal which was NOT clipping my interface, again, subtle but odd and hard to deal with in terms of gain levels on my interface, seemed i could never set the Kemper's volume levels correctly for certain profiles
4. Noise levels got extremely high and I thought my guitar was broken. Eventually I realized I could literally tap the tip of my gutiar cable on a table and hear it easily through my speakers.
5. odd high note aliasing tones which people are posting about
I did a system reset, midi reset and finally gave up, was ready to send the unit back. In desperation I performed the Flash Memory wipe as such:
1. Degrade firmware to 1.04,
I believe latest 1.08 does not allow getting into the system maintenance menu
Erase the internal flash memory
Note: ALL the rigs will be erased during this procedure!! ( credit to billruppert)
- Switch the main knob to off
- Hold the left/top soft-key above the LCD
- while still holding this key - switch KPA to tuner
- Maintenance Module will be started
- In the 'Maintenance' menu goto 'Memory'
- Use Memory FormatFlash and InitFlash
- Check if the KPA works (booting, tuner)
- Check all the KPA settings
I will add, go into the SYSTEM block and hit Factory Rigs right most soft button. This restores all factory defaults.
After this your Kemper will be fresh, like new, and more importantly have cleaned out FLASH memory and should work flawlessly! 
All my problems have been solved meaning no noise, no popping, gain controls are perfect, output levels are perfect, high note aliasing noise gone. Maybe this will help someone else reslove their Kemper issues.
