New Post: WTV with comskip doesn't preserve surround sound

I want to convert my wtv files to mp4 while cutting commercials with comskip while preserving the 5.1 audio track. It works without comskip just fine. Enabling comskip, I no longer get surround sound. My solution as of now is to run two conversions. The first one removes commercials and outputs a WTV. I then use the commercial free WTV to run conversion to MP4. Doing this, I get a commercial free MP4 with 5.1 sound. I'd like to skip the first conversion and just go straight to MP4. Anyway of doing this in one conversion with comskip enabled? I've tried both MEncoderEDLSkip=true and CutMP4Alternate=true to no avail. As I mentioned, it works without comskip, but that is less ideal. Any insight would be helpful.

First profile is WTV Unprocessed

Here's the second profile.
[MP4 Fast-modified]
Description=Fast MP4 (H.264/AAC) conversion. Fastest conversion but lower quality, more sensitive to errors in the source video.
order=handbrake
handbrake-general=--strict-anamorphic --modulus 2 --verbose=2 -f mp4 --decomb --detelecine -4
handbrake-video=-e x264 -b 1500 -x -r 23.976 --cfr cabac=0:ref=2:bframes=1:weightp=0:8x8dct=0:trellis=0:subq=6:me=hex:b_adapt=0:threads=auto
handbrake-audio=-a 1,1 -E faac,copy -B 160,0 -6 dpl2,auto -R Auto,Auto -D 0,0 --gain=0,0 --audio-fallback ffac3
handbrake-audioac3=-a 1,1 -E faac,copy -B 160,0 -6 dpl2,auto -R Auto,Auto -D 0,0 --gain=0,0 --audio-fallback ffac3
handbrake-ext=.mp4
handbrake-audiodelay=skip