I had a similar problem, the left shift key appears to be damaged, it doesn't feel 'right' when pressed. The machine works perfectly with a USB keyboard. Apple are only interested in replacing the whole keyboard, and say they may need to replace the top cover too. Not cheap! I'm not too confident about fixing the key myself, so I used a software fix.
I downloaded and installed KeyRemap4MacBook, then disabled the left shift key, clicked on the 'Reload XML' button, and all now works OK, except i can only use the right shift key, which isn't a huge issue. Caps lock is still OK.
This fix is at the software level, so you still need to hold down the option key to bypass safe boot. You also need to go into the system preferences and add KeyRemap4MacBook as an application that should start on login.