The /misc/ folder of the Piwik installation folder contains a .htaccess that basically blocks all access to the folder and it's subfolders.

However, the /misc/usr/ folder contains files like the custom logo that can be set which of course needs to be accessable by a normal HTTP GET. Therefore, the /usr/ folder has it's own .htaccess file which (re-)allows access to static files like e.g. PNG or JPG images.

The problem is that the code in the .htaccess file of the /usr/ folder does not unblock access to these files in all cases; there are various conditions that seem to allow access to the files for various server configurations but in my case these are not sufficient. I had to add the following code before the closing tag to make it work:

<IfModule mod_access_compat>
        Order Allow,Deny
    Allow from all
</IfModule>

Maybe someone with profound Apache knowledge should take a look that that file in order to make it more compatible. Because otherwise the custom logo is not shown in the Piwik GUI!