A digital pen that has a writing tip includes an ultrasonic (US) transducer on a pen body that generates frames of US pulses toward a receiver base in response to an infrared (IR) synchronizing signal from the base. The first pulse of a frame is adjusted by a modulo of the US period &tgr; when the time of arrival (TOA) of the first pulse varies from an expected TOA by more than one-half &tgr;. The TOAs of successive ith pulses in the frame, which are one wavelength apart from each other, are adjusted forward in time by subtracting from each pulse TOA (i−1)&tgr;, and then several of the adjusted pulse TOAs in a single frame are averaged together to determine a frame TOA. The frame TOAs from plural receivers on the base are then triangulated to determine a pen position for that frame, with the pen positions being input to a handwriting recognition module.