i suspect it might be related to the way how mplayer pauses the sound
   and then restarts it.


possibly.  sometime a year? or so ago i had to change my mplayer
config from autosync=30 to autosync=100 otherwise i found that
it regularly had audio pauses and sync lossage.  mplayer normally
uses timing on the audio write() to figure into other calculations
and setting autosync higher reduces how much it factors in.  so
perhaps this is now write() returning after different intervals now
than it used to?  ie, used to be consistent with the old kernel and
now has less consistency with the newer kernel?