I am trying to set up my Denon 3805 with Harmony 880 for multiple audio inputs.
I connected cable box audio to Denon via Optical 1 and set that as Input to VCR1 mode.
I connected Apple TV audio to Denon via Optical 2 and set that as Input to VCR2 mode.

I programmed my Harmony 880 and when I want to watch one of those, the receiver is set right mode (VCR1) but after few seconds it gets switched to DVD or some other mode.
Also, when I change the volume on Harmony that mode gets changed to VCR1 stereo mode. So, I loose audio unless I manually put receiver to VCR1 mode using Denon remote.

Can someone please let me know how should I program my receiver and harmony to make it all programmed. Where do I set/program, on receiver to say that for VCR1 use AUTO or DD Prologic Cinema mode etc?

Thanks in advance.

first make sure that you have configured your Denon to accept the optical connections for each of those inputs.
second the "auto function" on the receiver is for detecting the audio signal coming in weather it be for optic, coax, or analog.
third when using these inputs for sources that are meant to be listened to in surround sound leaving the receiver in DD/Prologic make the most sense as the receiver will see the incoming signal and default to the proper processor, i.e. DD, DTS, prologic.
finally if the receiver is only acting odd when you use the harmony remote, you need to reconfigure the software, or possibly just re-download the file to the harmony. if these fail you may have a bad remote (not uncommon with harmony) or you may need to get the assistance of a professional installer.