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This is probably a ridiculously easy question to answer.

No matter what combination I have CueMix FX in, I am continuously hearing signal into inputs 1 and 2. If I have both channels muted, I am still hearing input 1 on the left channel and input 2 on the right.

I have these channels muted on all eight busses.

If I have them unmuted, I see the signal in Analog 1 and 2, Mix 1 and Main Output.

If I have them muted, I see the signal in Analog 1 and 2, nothing in Mix 1 and signals at Main Output.

Even if I assign all busses' outputs to None, I still hear inputs 1 and 2 through the Main Outputs and see them in CueMix FX on Analog 1 and 2 and Main Outputs meters.

I have a good handle on CueMix FX, so, it doesn't seem to be any usual things to try. I have all of the other functions off (I don't have any exotic Stereo modes selected, I do have both channels' pans set to zero, I don't have overload protection on, Talkback is not enabled, EQ is off, Dynamics are off, Reverb is off).

I have MOTU Audio Setup set to:
Default Stereo Input: set to Inputs 1 and 2 (no matter what I change this to, it does not solve the problem).
Default Stereo Output: set to Main outputs.
Phones Assign: Set to Main outputs
Return Assign: Set to AES/EBU 1-2
No matter what I set these to, the problem is still there.

This is a Black Lion modded unit. Is it possible they accidentally or on purpose jumped something that's causing input 1 and 2 to always be heard through Main bus (Main outputs and headphones)?

You have so many monitoring options, both hardware and CueMix, it's hard to know where to begin other than the manual.

https://cdn-data.motu.com/manuals/firew ... de_Mac.pdf

I would look first at pgs 42 and 72 to see how you are monitoring the hardware. This would be my first guess.

You may have to reset to factory defaults first — let's hope not. pg 44

Thank you, Mike! Neither of those pages addressed the issue. I played with those settings to try just Incase. This is happening even without DP running. The Main and Headphones are mirroring each other. Somehow inputs one and two are bypassing all mute functions and also ignoring pan settings. The trim knobs, pad and phantom power are working, so, it seems that the input section of the 896/CueMix is working, but, the mix section isn't completely working for those two channels. If I unmute those channels, they are monitor twice the signal. The regular way (Pan/Fader/Mute) that the mix section works plus the signal that is ignoring that part of the 896/CueMix

This is a long shot, but do your problems occur even after rebooting the interface and the computer? I have issues with the mixer page not responding to changes after long periods of time. This might not be your issue, though.

I appreciate the question. Yes, it still happens after rebooting the computer and/or rebooting the interface.

I figured out what was happening. I have an Aux using Hardware Insert coming into the Mac/DP from my secondary 896 for my plate reverb. Because I only use 896 "B" for plate and tape machine, I usually don't have it turned on. When creating a new template with 896 B off, it's reassigning that input to 896 A's inputs 1 and 2.

It's almost always user error.