These warnings should not be a problem, indeed.
But they indicate something that might be a symptom of something else.
I'd recommend you clean up completely your Brainstorm installation if you have more issues:
- Edit your Matlab path, and remove everything that is not related with the Matlab installation itself
- Close Matlab
- Delete ALL the brainstorm3 folders that you have on your computer
- Download a new version of Brainstorm from the Download page of the website: https://neuroimage.usc.edu/bst/download.php
- If you have installed the program correctly (e.g. not setting up your database within the program folder) you wouldn't lose any data or your user preferences (which are in your $HOME/.brainstorm folder)