Let's start with your OS and version of ID, then tell us if you've set the page size from within the Print Booklet dialog (you have to click the setup button to temporarily leave the dialog and get to a print dialog).
I am using Indesign CC running on Win7
My page size is 8.5 x 11
My paper size is 11 x 17.
IF the s/w can talk to the printer, it does booklets and sets them out properly is one uses something as mundane as WORD.
What's the trick here?
In the Print Booklet dialog press the Print Settings button and set the page size in that dialog to 11 x 17 landscape.
And don't attempt to use the Canon's booklet module from Print Booklet.
If the Canon has a finisher that can fold and staple, I think you'd do better to export the file to sequential pages as a PDF and print from Acrobat.
If I set to the page to 11 x 17, I get: Printing error: adobe print engine failed to output your data due to an unknown problem.
I will persevere with Acrobat, but I have had some strange results so far.