After upgrading mplayer2 to 2.0_p20120517 it started having problems with (un)pausing and seeking, but only when set to use pulseaudio output. It seems to have hard time keeping audio and video in sync for a few seconds after unpausing or seeking. The video speeds up and slows down repeatedly while it tries to resync it. I also noticed, that audio continues to play for a short while after pausing. All of it happens only with pulse output and disappears when switching to alsa.
Please report problem upstream.
http://git.mplayer2.org/mplayer2/commit/?id=de435ed56eafee040fe286151e51b94c144badc7 Please try media-video/mplayer2-2.0_p20120815
Sorry, I forgot about that one. mplayer2 seems to have many different problems with pulseaudio (and they change every release), but this particular one is fixed by now.