Either all four tracks are separated 1/2/3/4, but then each track is also set with a preset of a lower bitrate (160) and the wrong 'downmixer' setting. I can set Handbrake's audio preset to automatically detect the four tracks in two different ways but both have the same issue. The issue is QoL as it gets old when I have to manually change 3 options for every clip when I'm compressing 50+ clips at once. I don't have complete control over the audio presets when I'm converting multiple clips at once. File sizes plummet and quality stays near identical. For its use Handbrake has been FANTASTIC. Currently I record with OBS, split and cut with Avidemux, then I compress the file with handbrake. My goal is taking gameplay clips/videos I want to save and compress them for storage and use later. So I'm looking for an alternative to Handbrake and I would love any suggestions. Also make sure you save/update the preset you're using after you configure the defaults. You can change the core settings to better suit your needs, but the 'Track Selection Behavior' and 'For Additional Tracks' are the key options. I recommend making sure you have the newest version (1.0.1) and these are my audio settings that are working for me. In case anyone else is having this issue with videos that have multiple audio tracks. If I ever get tired of Handbrake I have some backups. Yay! Thanks again everyone for your recommendations. With the newest release I am able to have my default audio settings exactly how I want them when I add files. I installed the newest version (1.0.1) and it looks like they updated the audio settings.

Before I even posted on the forums I realized I had an old version of Handbrake. So I solved my problem and I get to keep using Handbrake woo! So I figured I would go with u/unknownsoldierx's idea first and ask around the Handbrake forums.

Handbrake alternative windows