I would agree when the cut is off on the scan as it's normally down to that. This one is on the feed though, so the linear encoder shouldnt make a difference to that
I jump into this and hope my info will help.
I had an issue a while ago, the printing was skipping about 3 millimeter, but it was about every 12" apart, I was going crazy, until I check the motor behind the control panel on a Roland RE 640 and found out that a little drop of ink was on the "disk" (I believe this is also an encoder disk), the one that has the information same as the encoder strip, but in a circle, that reads the feeding, when the sensor got to that ink spot, the machine was not printing and skipping that part on the paper, leaving an streak of no ink.