There may be no problem at all. Even the kings of oscilloscopes, Tektronix, rarely had a calibrator output that was accurate as far as frequency. Amplitude, yes. Frequency, no. There were one or two models that actually had a tweak for setting the calibrator frequency to exactly 1KHz, but that was very unusual for them. Check your timebase against a known-good frequency source, such as the low voltage output of a mains transformer (60Hz in the U.S., 50Hz in the U.K.) or better yet, the output of a crystal oscillator.
Dean