This problem is inherited from Ubuntu 12.04, it wasn't present in 11.10 and seems to be fixed in the beta for 12.10, though I can't find any triaged versions of the bug to explain the fix.
It appears to be an issue with ALSA and Realtek sound cards where ALSA doesn't automute the speakers when something is plugged into the headphone jack, instead sound comes out of both. If the headphones are plugged in and then the computer is suspended, coming out of the suspension will make the speakers mute and sound only come out of the headphones, though once you remove the headphones, sound does not resume coming out of the speakers. So it's either a failure to detect the change or a failure to do anything about the change.
If this problem is in ALSA, it might be wise to backport the version of ALSA from 12.10 into Luna, or users, myself included, will have to suffer from this.
This kind of problems is typically caused by ALSA itself.
I'm afraid we cannot backport ALSA version from 12.10 in elementary OS because every version has its flaws and will not work somebody's use cases, but the one shipped with 12.04 is at least tested by Ubuntu, while we cannot afford a representative regression testing. Besides, the 12.04 version will be supported for much longer than the one in 12.10 and we cannot potentially deprive kernel-related systems of security updates.
So I'm marking it "won't fix" for elementary OS, though you can request cherrypicking this particular fix to 12.04 version in the relevant Ubuntu package (https:/