Thank you for forwarding on the issue to the Prezi Engineers and resolving the API issues so quickly.
Another difference with the API is the order the events are called. This is specifically a problem because now the contentready event is called after the first page is set to 0. Also, previously the contentready event was called twice. Once upon initial load, and once when all of the content was fully loaded. This is a problem because I observe the currentStepChange event, and since it fires before the content loaded event, step 0 is actually loaded first instead of being able to set the slide and then having it go to that immediately like in the old Flash version.
Additionally, Prezi API does not run in IE9 or IE10 anymore. There is a warning about unsupported debug method in one of the CDN api/files under prezi-a.akamaihd.net/landingdjango-versioned directory.
If you want to test the API the same way I do, you can go to PreziSCORM.com, enter a Prezi ID or URL and click download. Then create a free account at cloud.scorm.com and upload the course package. There is an “Add Content” button in the upper right corner. Click on that and then select “Import SCORM…” Next upload the package. Next select “Library” from the left hand menu and click on the uploaded course. Then click “Launch” and the course will launch in a popup window and allow the popup windows from the domain if asked. Finally, navigate through the Prezi until you get to the last page and a popup window will be displayed and you can click close.