The fact that the agent is still set to ‘last.fm’ tells us that the OP doesn’t have an issue with musicbrainz.
The program code for the last.fm agent is not maintained anymore. There won’t be any further developments or bugfixes.
Try if you fare better when you actually use the new program code.
See this thread where I recommend to set up a test library and point it to the same files. You could do the same and watch the outcome: Music Scanner scrambles and omits tracks on Multi-CD sets
