Printing apparatus (20) includes a continuous blanket (24) and a set of motorized rollers (31), which advance the blanket at constant speed through an image area. Print bars (38) eject droplets of ink at respective locations onto the blanket in the image area. Monitoring rollers (42), in proximity to the locations of the print bars, contact the blanket to be rotated by blanket advancement. Each monitoring roller includes an encoder (44), which outputs a signal indicative of a rotation angle of the monitoring roller. A control unit (40) collects, during a calibration phase, the signal from the encoders over multiple rotations of the monitoring rollers, detects a deviation of the signal from the encoder relative to a clock signal having a predefined frequency, and computes runout correction factors. During an operational phase, the control unit applies the runout correction factors to synchronize the droplets ejection from the print bars.