WordPress Installations in Subdirectories / Domain Mapping /Permalink Trouble

Hi there,

I have a number of WordPress 3.6 installed on three locations on my domain:

domain.com/folder1
domain.com/folder2
domain.com/folder3

These are separate installations, no MU.

Example 1:
mywebsite.com is registered at the hoster itself an mapped directly to domain.com/folder1.
Wordpress adress: mywebsite.com
Site Adress: mywebsite.com
Permalinks are working well.

Example 2:
myotherwebsite.com is registered at a different registrar company. I am using a URL forwarding / URL hiding (hidden forwarding) to the directory of my second installation domain.com/folder2.
Wordpress adress: domain.com/folder2
Site adress: myotherwebsite.com

Here is now my question. In Example 2 I am not able to change the permalink structure. The only possible structure is the default set with numbers. htaccess is correct and writable. The problem is obviously the domain forwarding.
Adding domain.com/folder2 as Site address instead of myotherwebsite.com works, permalink structure can be changed. Changing back to the right name/URL of the blog (myotherwebsite.com) makes it impossible to update the permalink structure.

I am really fighting with this topic for days, hope someone can help here. Thanks in advance!