I once thought it would be a good idea to put felt on the bottom of the front pressure bar (? bar that holds down the job as it goes into the laminator) of my laminator. I thought it would work well to clean the laminate as it held it down. To my dismay the first job I laminated was perf...the felt picked up wet the ink inside the perfs (ink never dries on the wax paper) and smeared it all the way down the job.
Based on this experience I would have to ask if perhaps you're picking up ink from inside the holes.