I do not know if this works with all radio / KPA1500 combinations however with my K3S/KP1500 I do the following.Hopefully it i something as simple as this.
I do not use the ATU in the K3S.
Tune the ATU in each sub-band (CW, SSB, Digi) using the K3S in Tune mode and selecting ATU Tune on the KPA1500.
I believe the amplifier stores and retrieves the ATU settings on different band segments. It reads the transceiver frequency and switches to the correct ATU settings.
Make sure the ATU is in line by depressing and holding the ATU mode button on the KPA1500. If both LEDs (ATU In & ATU Bypass) are lit the amplifier is indicating that the antenna VSWR is low enough and the ATU is automatically switched out.
Maybe your friend is doing this already. If so, then he has a strange issue.