[TMDaines]

Sounds like reclock is not getting the info of the video stream from the filter chain. As to how to fix it: No clue. I'd approach it by going back to the basics and play with mpc first. Do a minimal setup with it (use included filters of mpc) and reclock as the audio interface. If that works, add the filters you are planing to use one by one, until it fails: analyze at that point. if it already fails from the start, check if its really using the included filters and not some system filters that may interfere. Remove or block them within mpc and try again.

Once you know what to do, you can do the same in Kodi, however, blocking filters is not possible as far as i know, so you may need to remove them.

I think I solved it!

Turning on "Use system filters (DirectShow merits)" lead to Reclock finding the video stream for all my files, which suggested it was indeed a filters issue. Also using MPC-HC's internal filters for MKV lead to Reclock finding the video stream for all my files when played in MPC-HC.

After an hour or so of changing different MKV-related settings in the LAV filters' menus, switching the Hardware Decoder in LAV Video from "Intel QuickSync" to "DXVA2 (copy-back)" has seemingly solved the problem!

I guess this begs the question: why is "Intel QuickSync" recommended over "DXVA2 (copy-back)" for Intel users in this guide? Am I potentially missing out on anything by making this switch?