Recording a window using the --windowid option, doesn't track the window itself, but the region that it
       covers.
       Also when using that option the -x,-y,--width and --height options are relative to the specified window area.
       An easy way to find out the id of a window, is by using the xwininfo program.
       Running a command like :
       xwininfo | awk ´/Window id:/ {print $4}´
       will give you only the id of the window(which should look like this: 0x4800005)
       More conviniently you can put all that in the command that launches recordMyDesktop like this:
       ~$recordmydesktop --windowid $(xwininfo | awk ´/Window id:/ {print $4}´)
           Also, the lower quality you select on a video recording ( -v_quality option), the  highest  CPU-power  that
       you will need.
       So  if  you  are  doing  the  encoding  on the fly ,it's better to start with default values and manipulate the
       end-result with another program.
       An excellent converter is the vlc media player, which can perform a variety of transcoding
       operations, either using the graphical interface, or the commandline for more flexibility.
       vlc is a complex piece of software, so you should consult it's documentation, before
       using it.
       An example follows, which will resize a recording named out.ogv to 512x384:


I created a function for my .bashrc file:
windowrecord(){
recordmydesktop --windowid `xwininfo | awk '/Window id:/ {print $4}'`
}

Once you run the function, all you need to do is click on the open window that 
you want to record and the window ID will be inserted automatically.