On the iPF9000 that showed that issue, after printing several miles of art papers, it was a lack of pressure on the pinch rollers that made media transport irregular.
Temporary solutions were made by inserting carton on the pinch roller forks to increase the pressure but we (me on the telephone) were convinced it had to be something else, Canon here had no clue. The media transport axle (I still do not know the right term in English) seemed to be below the media traject, 1 - 2 mm. A new one replaced the old one and did not solve the issue. In the end the nylon? parts that are underneath that axle were replaced by new ones of a different design, Canon obviously has encountered similar wear in other printers. The old parts had a small roll for the axle support and it rolled with the axle but no longer in that printer, wear on those rolls made the axle drop the distance we estimated. The new parts just have a slightly excentric support glider cushion where the axle turns on.
met vriendelijke groeten, Ernst
Shareware now:
Dinkla Gallery Canvas Wrap Actions for Photoshop
http://www.pigment-print.com/dinklacanvaswraps/six-canvas-wrap-actions.htm