I use WGT caddy which is basically a free non WGT Putter / Shot pal. What I have noticed though is that as with WGT caddy you have to set the 'size' of your overlay meter and you start with the right hand bar, i.e. the last line in the 'normal' meter bar before you get to the blue bar / ding line bit. Once you've got that lined up you fix the left hand side of the meter.
Well I lined it up and eventually got it perfect, imagine my surprise when the yellow 'release' bar, i.e. the thing that appears when you release the mouse button to start the meter, is NOT fully to the left of the WGT meter, it's only a pixel or two difference but that may be significant. Have a look next time you use the meter.
Edit, this isn't an issue with WGT Caddy, its the meter, if you hit a shot 100% the yellow bar drops down very slightly to the right of the extreme left hand side of the meter.