Delay between visual stimuli and (parallel port) triggers

(part2/2)
When I look at the time difference between the stimulus transition and marker, I still get this strange pattern. The (mean) differences between the red and blue values can be explained by the detection-threshold of the opto-detector.
deltaT_03

I find this pattern strange. If we look at the difference of the values, it seems as if the drawing/flip is out of sync with the actual drawing and flip…
deltaT_04

Any suggestions on how I can fix this strange behavior…?