Roon generally prefers roughly the number of items in a folder that you would expect with an Artist > Albums > Tracks structure.
There have been some improvements made by updates over the last few months, but there can probably still be problems with hundreds of subfolders in a folder, thousands of tracks in a folder, etc.
This is one of many posts by Roon staff about this:
As it seems to be benign for you with some folders not others, there may be something special about the latter that trips up Roon. I suppose it’s best for Roon support to look at this.