I have the ipf9400 and have had issues with ink coming off of synthetic substrate as well. (In my case it was a polypropylene psa). I spoke with my manufacturer and they actually made a custom media profile for me so that the printer wouldn't lay down as much ink. It doesn't produce the colors as accurately as I'd like, but at least it doesn't rub off. Maybe try talking to your manufacturer or vendor?
There are 9 different "Special" media types pre-built in my printer interface - not sure if its the same for you - but the profiles are actually a spectrum of how much ink the printer will use. I just forget if #1 uses the least ink or the most. I would try a strip test and print on Special 1 and and Special 9 (if you have them).
Try Canon's IPF tech support hotline 800-423-2366
Word of advice InDesign is great for layout but not the best for printing from, especially if you're using a custom media profile. I would rip a pdf and print from Acrobat. Make sure you chose "Let printer manage colors" from the color management section.
