Jtuttle
Hi there,
Thank you for your feedback.
SKYBOX should correctly detect the side by side mode of your videos. You can click Stereo Mode, manually select the SBS mode or click Auto and see if it helps.
What's more, if the folder name contains some specific key words, SKYBOX will automatically recognize the video as corresponding stereo mode. For more info, you can check this FAQ.
If possible, we hope you can share with us the side by side mkv movie for testing.