I am in a similar situation, though my main garage door opener actually is older. My 04 M3 has no issues with the main door, or newer second door opener.

Main door - older style dip switch style, NO learn button on the motor
secondary door - newer learning style.

I cannot for the life of me make the homelink in the 01 X5 we just picked up work. After reading all of the guides, it LOOKS like the homelink trains itself (from the light blink combinations) but nothing happens with the door. My 04 M3 has no issues with either, which combines the frustration for me and my partner's new (to us) car. I wish I could fix this for her.