I have the same issue and not only with DVD disks but with any other audio source. When I switch the audio to the TV everything is OK. When it happens I found that if you press few times the buttons on the remote for sound effects it fixes it but some time doesn't. I'm sure it wasn't like that before the last firmware update. I'm thinking to go back with one of the old firmwares if it's possible because the system is useless like that.
I purchased and installed the Samsung Bd-1250 HTIB back in September, and have had good experiences with it thus far. To test the blu ray at the time, I purchased Casino Royale, which worked wonderfully; no issues. I just now bought a new blu ray movie and within the first 5 minutes the sound cut out to all but a whisper (I assume the only speaker I could hear was either the center or either right or left channels; but not more than one). At first, I thought that the part of the movie was quiet and that what "sound" I heard was from a neighbor's apartment, cuz, it sounded distant and muffled. But, it wasn't; it was my set.
I stopped the movie, tested the speakers (the center seemed a little crackly, but it came through), and restarted the movie. The sound seemed "ok" but a little tinny - almost like the tv speakers - but the surround is working fine, so I know it's not using the tv speakers. Then, the sound cut in and out quickly again, though this time it, for the most part, stayed "on".
My TV is a Sharp Aquos 40" LCD, 1080p, 120hz. I also purchased it in September of this year.
To date, with regular tv and regular DVDs, I've not had any issues with sound.
But, I have heard that the blu ray player on this system tends to be problematic in many cases, so here I am.