Our solution was to put my site collection on its own Nintex Workflow content database. Since then all of the issues disappeared.
Our original issue was that someone on another site collection created a workflow that exponentially created records in a list until there were over 13 Million records and that created a huge number of logs and other associated content in the content database.
After two weeks of clean up by our admins, the problems persisted. So the new content database was the answer. By the way, I have a very large, busy and highly automated site collection and we were already on our own SharePoint content database. Hope this helps.
Regards,
Patrick