Hi @gmfbrown 
Sorry you’re having issues!
Just to knock one possible cause off the list - did you try to switch between speakers and headphones while Sonic Pi was running?
(It is currently not possible to change audio devices that Sonic Pi use while it is running, although we’d like to be able to allow this in the near future).
The ‘Raspberry Pi Audio Output box’ is not relevant for you, so don’t worry about that
Something that would be very helpful is if you can open up an issue ticket on our source code repository’s issues page, briefly explaining this problem again (you can just paste in the details you wrote above if you like):
There’s maybe a few more things we might be able to do to investigate this - I’m happy to continue with it over on an issue over there. (We find it easier to track potential bugs and do in-depth troubleshooting on issues on that page 
).