This just started yesterday for me out of the blue on songs I had listened to with no problem earlier in the day. Found that if I kill the Music app and restart it the problem goes away. Was fine last night and earlier this morning until 5 mins ago when it started acting up again. Killed Music again and restarted it so now it's playing with no issues. This is by no means a long term solution but will at least get you listening in short order.
Did you ever get to the bottom of this? I am seeing the exact same issue as you when using the headphone remote. It does not happen all the time, in fact it is pretty infrequent but it happened this morning. Unpause and I get one beat of the song, try again and the same happens. Third time and the song started to play but was skipping and stuttering for about 10 seconds. This was on a track I purchased from the itunes store.
Overall I am not as happy with my 4s as my 3GS. It just seems buggier.
I've had this problem since day 1 of getting the 4s. I took it to the genius bar and they suggested restoring the phone. I did, and it still happened. I took it in again and they gave me a new phone. But, it is still happening.
I've tried multiple headsets and this happens in any audio program. Pocket
Casts, Pandora, InstaCast, etc.
Very weird and annoying. Someone suggested it has to do with Siri. I'll try turning her off for a few days and see if that helps.
I am having the same problem on multiple iPhones. The 3GS is over two years old and the 4S is brand new. The software and firmware for both devices is up to date. For these reasons, I don't think it is related to the iPhone hardware.
It started very recently (June 2012).
It occurs on the headphone jack and on music systems that connect through the dock.
It occurs when using the stock music player application.
I am loading the audio files via stock iTunes, which is up to date. I wonder if it is realated to the last iTunes update.