This is one issue with borderless printing that I've mentioned to our Canon rep, and he's aware of the issue and has been talking to the technical department making the settings for the printer.
It also depends on which setting you use (based on the media; coated, photo, canvas, etc), that certain products will be cut more between prints than others. Hopefully this will be better set up with the new imagePROGRAF Pro series.
I've seen the same thing on our end using the printer between coated and photo products. Coated isn't as much, but photo and adhesive will be about 6-8" wasted media between prints.
If you're able to figure out a setting to shrink the amount, good job! Many people may be frustrated with the issue over the past 4 years, but Canon is surely aware of it.