On a clean OS install, the error you are reporting does not occur on the systems here at PreSonus. The error is resulting from a problem with some audio application or plugin that is installed on your system.
If you open up System Report and go to your System on the left column, and look at Logs, in the Apple System Log you should see an entry for something like this:
systemsoundserverd: kAudioUnitErr_TooManyFramesToProcess : inFramesToProcess=1115, mMaxFramesPerSlice=512
You may see other applications that are having issues as well.
An unknown (possibly audio) application in your system is causing the system to initialize Audio Units incorrectly causing a buffer overrun. Which is causing the AudioBox to fall off the bus and back on as the buffer gets reset.
Please check your other applications manufacturers websites to see that they have updated software available that supports 10.11.
We're not ruling out Mac OS X 10.11.1 either, however we've never seen this during the entire testing of 10.11 since the early betas right up to the betas we're running now. We have reported this issue to Apple as you are not the only person reporting this issue.
Apple has a technical bulletin about this error: https://developer.apple.com/library/mac/qa/qa1533/_index.html
If you find out what application is causing it, please provide an answer back here for others to find.