I have been running ISPConfig for a long time and have not had any issues. After upgrading to the latest version my Mail tab does nothing and when clicking on any link they do nothing. For some odd reason the error log shows its looking for the php pages in my webmail dir. Also the new feature APS does nothing and when updating the package list nothing shows up.
You have a alias for /mail in your apache config somewhere instead of /webmail for your webmail client. Change that alias bacj to /webmail and restart apache.
It was actually something else and I got that part fixed. Why is APS showing nothing when choosing to update packages?