How to repeat:
1. Start smplayer with any avi, mp4, etc.... in window (not fullscreen), press Play and resize window so you can access other windows on your desktop.
2. Set Option-Video-StayOnTop to Always or While Playing.
3. Set Option-Preferences-Keyboard and mouse-Mouse-Left Click to Play/Pause.
4. Click on any window on desktop so Smplayer lost focus.
5. Click on video in Smplayer with left button and system freeze for 3-5 seconds and sound begin to stutter during this freeze.
if you make addidional step like
4a. Click on Active title bar of Smplayer
and the step 5 - no problem at all, so seems this lag exist only if smplayer is "off focus" during click on active window for Play/Pause.
I've tried all versions starting 0.6.0 to 0.8.0 and found first time this problem appear in smplayer 0.6.10 (in 0.6.9 works fine)