I have searched through the bugs tracked here and there seems to be options for Linux users to fix the screensaver coming on bug. There are no answers for Windows users.
Version: 0.6.9 (r3447)
Using MPlayer r30369
When in full screen mode the screensaver comes on at the system specified time (15 minutes on my machine). When SMPlayer starts playing, the system time is set to 1 minute. This used to work when I used Vista and an older version of SMPlayer/MPlayer.