I've had this issue for many years, and it keeps reappearing...
Some MKV files have incorrect tags, so I update the tags and all is well. For some of these files, when I view them from other applications like Windows Media Center or VLC, the tags are still as they were prior to updating through MC. They are correct when viewed from MC. The strange part is that eventually, the tags revert back to their original, non-updated, values in MC. I can force this to happen by deleting the folder from the Library and re-adding it, forcing a re-import.
I suspected the root cause may be that MC is saving the updated tags to a sidecar rather than the files themselves. In Options->General->Importing & Tagging: "Update tags when file info changes" is checked, "Sidecar tagging mode" is "Save in both sidecar and internal tags (if supported)". I see sidecar jpg files for these files, but no sidecar XML files, leading me to believe that the tags are not being saved to sidecar.
Could this have something to do with read/write permissions for the files? All of the files are stored in shared folders on a QNAP NAS.