I'm thinking one of two things happend. Either someone changed the remote pairing address for the DirecTV and remote, or the way that they communicate (IR vs RF). Another possibility is somehow the Slingbox lost the remote profile that was installed during the Setup Assistant process.
You can check your DirecTV setup window, make sure its using IR and has remote address #1. The IR codes provided by Sling Media is configured with address #1. Also, make sure its set to Infra Red (IR) instead of Radio Frequency (RF) since the Slingbox comes with IR Blasters not RF blasters.
I think you hit it on the head. I was "attempting" to control two different DirecTV boxes with my DirecTV remote. I changed the DVR from receiver #1 to #3 as a test and forgot to switch it back. I'll give it a whack when I get home tonight.
BTW both DirecTV boxes are in the IR mode and not RF.