I figured out a hacky solution for the volume controls on my DirecTV remote. Basically, vsu is correct that the volume buttons send two commands in sequence so you have to get the Flirc program to record only as the second command is being sent. Whereas most buttons only light up the top-left light on my remote, the volume controls light up the top-left then the top-right immediately after and that seems to indicate when each command is being sent. My solution is to:
1) Hover the mouse cursor over the desired key to record in the Flirc program
2) Press the desired volume button on the remote
3) Wait as the first light blinks and then click the mouse as the second light turns on so that only the second command is recorded.
You may have to try a few times to get the timing right, but I now have volume up, volume down, and mute all working with the DirecTV remote through Flirc. If you click too late, just click again to cancel the recording and try again. Strangely the XBMC "mute" button preset didn't work so I had to manually set it to F8 in the keyboard controller.