I have never experienced this problem before, but it is now happening to me. Same MB. I could not think of a single thing I could have changed - until you mentioned BIOS version. If I remember correctly, this only started happening when I updated from F5 to F6. Going to downgrade to F5 to confirm this.
EDIT: Reverted to F5 and the problem persists! I am completely stumped here. Back to using front green port along with my back ports (5.1).
EDIT 2: I started the whole audio process from scratch. I have found the following to be consistent:
1. Audio with DSDT with Hdef changes as per Toleda's thread results in audio drop-outs on Rear Green Port using ALC887 Current version - Plugging the green jack into the front Green port = no audio dropout. This is with 5.1 sound enabled / disabled.
2. Without DSDT - ALC887 current with Hdenabler-1 = No Audio dropout on Rear Green Port. But 5.1 audio is not available. It shows in the Midi speaker config, but no sound through rear & centre. Multichannel output also only uses front speakers
3. Without DSDT - ALC887 current with Hdenabler - 2 (have to manually delete Hdenabler 1) - Audio dropout on rear Green. Disappears when using green front port. (5.1 & Multichannel work)
EDIT 3: Work-around found quite by accident. Was using skype and used the front mic & audio ports. When I finished, I unplugged the headphone out and forgot to move green rear back to the front port again. Been listening to music for over an hour now and no audio dropping at all. Then I noticed the mic from the headset was still plugged in. As soon as I unplug the front mic, audio dropping starts again. Plug mic back in and ... perfect! Weeeeeird! Now that I mention it, I think I always used to just leave the headphone's mic plugged in before.No wonder I never had this problem before. Oh well, that is a lot less painful. Now I don't have to have the green rear cable running over my desk to the front panel anymore! Not right, but functional.