Problem recording on two tracks

Hello everyone. I am doing some recordings using Cubase SE and I am trying to record something on two mono tracks simultaneously in order to do a stereo effect. A curious problem has arisen: while things are fine on one of the tracks, on the second one the part created is always shorter, by several hundredths of a second. It just appears shorter. Can anyone think of a reason for this to happen? It happens whether the recording is stopped automatically at the right locator position or by just pressing the space bar. I cannot think of any recording settings that are applied specifically to tracks. Am I missing something obvious? I tried recording three tracks simultaneously just as an experiment and in this set-up, again one tracks is correct and the clipping occurs on the other two tracks.