Can't Save as Template in iBooks Author 2.1.2

I've only just now tried to save as template in this version. This is what it used to do:
Replace the .iba extension with .ibatemplate.
Change to the iBooks Author Templates folder so that you can save there.
Now it doesn't do either of these. When you select File > Save as Template..., it presents the folder where the .iba file has been saved and does not change the extension.
Manually changing the extension and putting it in the templates folder gives it a generic Pages document icon in the Template Chooser. However, it can be opened as a template through this dialog. The title of the document is Untitled, just like it would be if a template were chosen.
Has anyone else seen this?
I have lodged a bug.

Thanks both Arnis and Mike --
Interesting suggestions from both of you.
Arnis, we're putting the cleanup utility on the back burner for the moment, since in our company, we can get in trouble using third-party software. However, it's good to know about this utility and we will use if it we have to. (Occcasionally we are forced to put our careers on the line for issues like this...)
Mike, we created a folder called "PDFSettings" in the 7.2 "fminit" folder and copied over the six joboptions files from 9.0. Rebooted, rePDFed and voila, that worked. (Mind you, we can't say for sure that's what worked, because as I said in my original post, the simple act of rebooting "sometimes works, sometimes not...")
Eventually this problem will go away by itself because eventually we will get rid of 7.2 -- it's only deadline time-crunches that have made us reluctant to jump fully-clothed into 9.0...
I really appreciate the two of you taking your time to offer suggestions and help. I can't imagine life in the FrameMaker world without you!
Cheers,
Gay

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