Periodically, we host what we call Celebrity Chats on our site, during which we bring in well-known personalities to chat with our members. This often causes a brief spike in traffic, typically lasting a couple of hours -- exactly when we would most like to have WP Super Cache working for us.
Unfortunately, this plugin conflicts with the SD Questions & Answers plugin (http://wordpress.org/extend/plugins/sd-questions-and-answers/) we use as the infrastructure for our chats. As long as Super Cache is active, the chat session simply does not appear at all. Disabling Super Cache solves the problem immediately.
When we first noticed the problem, I systematically disabled all of our other plugins one by one, since we use AJAX in many parts of our site. Only Super Cache causes the problem. (Incidentally, W3 Total Cache does not conflict with SD Q&A, but neither does it improve our site speed much.)
SD Q&A once had a conflict with another plugin we were using, because that plugin had an outdated Jquery library. With the help of the plugin author, we updated the Jquery library that plugin was using, and SD Q&A worked just fine thereafter. (We have since deleted that plugin.) Is Super Cache by any chance using outdated Jquery?