Every time I attempt to save output as JPEG, CS6 is substitutes the .eps format and puts up the EPS options dialog.
Has anyone seen this before? What is going on and how can I fix this?
You're on MacOS, and mistakenly copied file format plugins from a previous version of Photoshop.
Go delete all the plugins you copied from a previous version of Photoshop, or turn off the additional plugins folder preference that you pointed to a previous version of Photoshop by mistake.
Thanks Chris, that was indeed what had happened.