I have tested your Questionnaire module from your test site and tested in my system. Here are some problems / bugs that I have encounter during the testing:
Problem  Cannot edit the Questionnaire Template after clicking the Finish Questionnaire. Probably can develop a 'Questionnaire Template Manager' to manage Questionnaire Templates where admin can edit (save, delete, modify and whatever) the Questionnaire.
Problem  There is no 'Save Question' button when editing question. Should have a 'Save Question' so that it will looks much more user-friendly. (Please refer to the picture attached)
Problem  No Hint/Help for the 'Finish' button. (Is the Finish button also known as Save Question? or it only simple just go to the main page of the course? (Please refer to the picture attached)
Problem  Cannot delete Questionnaire listed under the '- Copy existing: ' and '- Use public:' Should allow delete of Questionnaire or some kind of management of those Questionnaire listed in there. (note: Logged in as Admin)
Problem  After clicking Finish, the Questionnaire was not shown on the course as a activity. (note: Used Admin account to create the Questionnaire.)
Minor Problem  Under Editing Questionnaire - General Page, the Help button was not available for those buttons at the bottom of the page.
Wish List  Have course-mapping features (similar like the feedback module)
Tested Questionnaire module version: 2007010801
Tested on Moodle system version: 1.7.2
Please kindly let me know if there are any special settings required to solve the problems above. Thanks.
(Can see that the Questionnaire module have improve quite a lot. Keep up the good work! )