Exact placement of print lines is extremely important to reduce density banding and color misregistration in a high-speed thermal tandem printer that employs separate print stations for each color. We propose a flatbed scanner method for precisely estimating the errors of line placement and print velocity. Our approach uses a model for the scanned data that translates line placement errors into phase variations. A classical phase estimation algorithm is then employed to robustly estimate the line placement error in the presence of print artifacts such as noise and thermal history effects. The optical distortion of the flatbed scanner is measured and the spatial frequency bands that contain large scanner errors are excluded from the analysis of the printer. We present examples that show the usefulness of this method in identifying problems in printer transport systems, and in verifying the effectiveness of solutions to these problems.