Hi Melissa,
Firstly, welcome to the community, great to have you here! 
Are you using the unified board list or the old left pane which splits the folders/boards into the 3 types of boards?
We are about to release this to everyone so if you would like to try it, you can activate it from monday.labs now.
However, this new version will still have all shareable boards appear outside of folders for guests. We’ll be happy to pass along your feedback to our product team to consider changing this in the future.
Boards shouldn’t pop in and out of folders so would like to understand this point better. We’ll email you via support@monday.com to get more information and check it’s not a bug.
Thanks!