I'd still give my ffmpeg command a try. Swap mkv with mp4. Or maybe convert to mkv? The only thing that makes sense is that there is something off about your files since transcoding fixes it.
Jellyfin 10.10.3 (Docker)
Ubuntu 24.04 LTS
Intel i3 12100
Intel Arc A380
OS drive - SK Hynix P41 1TB
Storage
3x WD Red Pro 6TB CMR in RAIDZ1 (JF Library)