What I noticed is the following: ( if it didn't change since then )
- when downloading the 1st time the track configs, they are in config/tracks
- when starting a session with one of these tracks .... this track, afterwards, appears in the config/tracks/loaded .... allowing to open the next sessions quicker.
- when updating this same track in config/tracks .... the older one remains loaded and the update is not applied in game.
Now, how it happens when updating with CM ... I don't know.
When doing it manually, rather directly place all track configs immediately in config/tracks/loaded
In your case, Billy .... I'd copy all files from the config/tracks to the config/tracks/loaded folder. That way you'll be sure to have them all and with the latest updated ones.
EDIT:
I just made a test with updating a single track config in CM .... the install of the new config is done in the "Loaded" folder.
So ... the problem only happens when updating with a manual full update downloading from Github and copying immediately in your install.