Did you manage to fix this? Was it a hardware issue and did the touch pad need replacing or could be cured with a PRAM/SMC reset, format/reinstall?
I have a similar issue. I too use the bottom left as left click and bottom right as right click. I got my Macbook Pro 15" Unibody in august 2009 and it was fine up until around october 2009. It now is a bit intermittent. Around every 4th or 5th left click it doesnt register and I have to click again to make up for it. Extremely annoying. I need to use the left right thing as I prefer using my touch pad with one hand, hate having to do the apple right click thing holding a key down with a central click. It's just not ergonomic.
If it hadn't been working great in the past I'd have just thought it was a 'feature' of left and right clicking, but because it did work fine I fear the touch pad could be dying.
I'd like to know if you solved the problem or if anyone else has solved a similar problem. Intermittent mouse clicks are soooo annoying, especially on a £2k laptop!
It's also annoy as you could be dragging something and the click would randomly stop and you would drop the item, even tho the mouse button has been phyiscially depressed the whole time. Can screw a lot of stuff up when you do a simple drag and it drops into a random folder
Spec:
August 2009 Macbook Pro 15" Unibody
Multi touch glass touch pad
Left and right clickable areas enabled
Snow Leopard - Fresh install not upgrade.
No other mouse software running that could influence the touch pad behaviour.