The Compass story sounds totally bogus, I've always had DL's regional airline BPs printed when it's a DL flight number which it should have been.
I did find a work around, but it's still weird. If I try to check in for the trip, I get the BP for SFO-ATL but not the second leg. However I can click on the "check-in" link in the upper right where it asks you to put in confirmation # and departure city (not from My Trips). If I put in my confirm and ATL as the departure city, it allows me to check in for the second leg and print a BP.
On a side note... I was able to get 2 HOOU certs this way... lol.