You know what, its fine. You have the motor on the top of the exhaust stroke. The crank needs to be turn one full turn and those dots will line up just fine.
Well I was thinking the same thing but let me say this. I am making sure the rotor button is on the #1 cylinder wire and I can see the piston is at it's peak in the bore and also both valves are closed. I have done this about three times and the dot on the cam gear is always at top and the crank gear is on always in the same spot. Does that sound like I have found TDC?