I'll help you if I can, but I'm not certain what question you are asking?
Are you not able to see the missing tooth portion on the scope?
For reference, here is a scope shot of my 36-1 wheel, and my single tooth cam sync.
http://img7.imageshack.us/img7/64/camsyncee9.png
As you can see, the red trace is the 36-1 wheel, and blue trace is the cam sync.
It's important to capture the steep crossing through zero. So in the cam sync, it would be steep through zero on the way down, from positive to negative. This is the direction coming from sensor. You must distinguish what your VR circuit is doing to the signal when it arrives at the IRQ as a square wave, which is what the software decodes. Conventional V3.0 circuit boards invert the signal from signal to IRQ, so this trace should be programmed for going high (which is backwards from what you see at the sensor).
On the 36-1 trace, as you can see, you can't distinguish polarity unless you look at the missing tooth portion. In this pic, the red trace 'floats' up at the missing tooth, and also has the steep crossing from positive to negative. Again, important to consider whether the VR circuit inverts the signal when arriving at IRQ as square wave.
Can you share the scope shot that you have?