Don't turn the option "Press the stop button once resets the time position" on, this option will make smplayer unable to remember the play time position when it's shut down.
At least this happens to me (Xubuntu 14.10 xfce, smplayer 14.3.0)
Hi. I had the same problem. Was working and then an update reset my preferences. For me the solution was: a) in Preferences/General check options to remember settings and time. b) in Preferences/Playlist uncheck option to Play files from start (this was checked by default).