In the beginning I had the same problem. But with a bit "trial" it's easy:
1. Just select a desired band first (manually) and pick the antenna from selector. If needed, set the rotator into a new position.
2. Then go to scanner and unclick the same band, then click it again to make it "active" (green LED is on). Set the "Ant Mode" to "PROG".
3. Start the scan and it should be working well. :-) Each band toggles the new, saved antenna for this band.
Bands without antenna-saving will go back to the standard IDC. Next band with a e.g. Yagi or Cardioid will activate the rotator.
73 and good DX from Jörg :-)
JO31ok
Bochum / Germany