The azimuth may have been off on the record machine.
Start by putting up you MRL alignment tape and make sure that your machine starts on. The Lissajous pattern should be the right phase relationship for all freq.
If say, 100Hz and 10kHz are right, but 1kHz is out, just put up the 10 kHz tone and adjust the azimuth watching the pattern shift in and out of phase while the meters on the machine climb in level.
When the meters peak, go back to the 1kHz tone and adjust looking at the scope so that the Lissajous pattern is in phase, then do the same for the 10kHz tone. 100Hz should also look in phase.
After you're sure the azimuth is correct on your machine, then put up the client's tones. If it's still out at 1khz, but fine at 100Hz and 10kHz, you might be able to adjust 1khz so that it's in, but most likely the record machine's azimuth was out when the tones were printed and there isn't anything that can be done to rectify that.
Cheers,
Cheers,