My problem is: I have a huge data directory (400GB) from a website and have a second website enabled for the new design, where I have symlinked the data directory.
Now there are some file checks using
$processUser = posix_getpwuid(posix_geteuid());
So, I solved the problem. My fault was that I was searching for errors from bottom layer to the top, cause I thought it was a permissions problem.
After many try and fails I found the not very obvious "option" panel in ISPConfig, where you could set some openbase-dir values for the clients webspace, which was chaining php to the directory. Now I just added the "main" webspace holding the 500GB data directory to the "child" webspace with the symlinked directory and its working like a charm.
Warning: my PHP was writing out with umask(022), so the group was only able to read, if you write out on the child "webspace" you have to set the umask to (002), so group is allowed to write to.