That sounds quite strange - are you sure you have upgraded all your files and haven't left any old files in place? - I've just tested a fresh 2.6 install and adding a Course, selecting "single activity" as the course format, then "SCORM" as the activity works fine. Have you previously used the single activity course format (it was previously a 3rd party plugin for Moodle 2.5 but is now a core module)
Also FYI - you don't need to use the course format to add a SCORM activity - you can add a normal course format (single/weekly) then use the add an activity link inside the course to add a SCORM package to your course.