ACL settings for civicrm in Joomla cannot be reset anymore
After updating Joomla 3.5.1 to the latest version Joomla 3.6.0 this problem seems to have disappeared completely.
I checked a civi 4.6.19 and a civi 4.7.9 install and both behave well again. You can now change the AVL settings again.
I did hear that the acl-part of Joomla needed and got some TLC so I presume this was the culprit in the previous Joomla version.

I did not need to to set the value of 'max_input_vars' (default 1000) higher for this to work.