I use for my slave site a different media directory.
html/joomlaMS/multisites/mySlaveSite/images/....
For the 'stories' it works fine but for /images/banners folder it does not point to the slave folder but to the master media folder in html/joomlaMS/images/....

Is there somewehere an other/extra setting for the banner folder?

Can you be more explicit on which Joomla administration screen and field where you have this problem.
If you can give a screenshot, this will be very good.

Can you also indicate if you have deployed the website into a specific directory ?
As you have specified a different media directory, can you give us the name ?
it seems that Joomla has hardcoded the directory path /images/banners.
If this is the problem, this means that this could be a Joomla bug that is perhaps already reported.

Can you also indicate if the slave site directory defined into the hosting server use the same directory path than the master or the potential speicifc directory used for the deployment ?
If the slave is assigned with the master directory, perhaps a solution could be to use a specific slave site directory (/multisites/xxxx) and use the /multisites/xxxx/images directory to keep the Joomla rule that consists to use the "website root directory" /images.
If you slave site use the /multisites/xxx/images directory, this Joomla hardcoded parameter will become a specific one.

Yes it seems that the /images/banner folder ist hardcored.
I have seen that Joomla has hardcoded the directory name /images/banner and not use the Global Configuration media folder. If this is the field where you have a problem, this mean that Joomla itself has probably a bug as the configuration directory is not used correctly.
If this is the field, that is probably a work around if you deploy the slave site into a specific directory and that you configure your hosting server with this specific directory
I did deploy the slave site in a "specific" directory and i did configure my hosting server with this specific directory. But because most of the directorys pointing via alisas to the mastersite the hardcored setting of the master is used to specifie the banner folder. That's the way it works I believe? The simplest workaround is just to use for all sites the same banner folder.
As long joomla does not change from hardcored to the Global Configuration media folder.
But I don't really understand why joomla uses the master root for the the slave instead the slave root html/joomlaMS/multisites/mySlaveSite:S ? Because I configured my sitename to html/joomlaMS/multisites/mySlaveSite.

The reason, is that Joomla compute the name based on the real php file location.
Therefore, when a symbolic link redirect a PHP code to the master directory, the location that is returned by PHP is the master path.
I have already work with a customer to develop a work arround that has been operational for this specific customer and that I would like to certify before releasing it.
As it the patch is very sensitive and for the moment OK for customer specific, I have not yet included into JMS due to the potential side effect with other extension.