Ignition timing
One of those TDC's is between the exhaust stroke and the intake stroke ("overlap tdc"). That's not the one you want. The timing LED isn't going to behave correctly if you're on overlap TDC.
The other TDC is between the compression stroke and the power stroke ("compression tdc"). That's where you need to be, in order to static time the motor
So if you just put the vertical line in the window, without knowing which TDC you're at, you have a 50-50 chance of being on overlap TDC instead of compression TDC. Rotate the motor one full rotation and try again.
We see guys make this same mistake all the time when adjusting their adjustable pushrods. When you adjust your pushrods at overlap TDC, you end up with a lot of slack in the valve train, causing noise and generally galling the hell out of the valve tips. We've even seen guys who've done this then go trashing their head porting shop online, claiming they were sold defective parts. One of many reasons we put guys into non-adjustable pushrods and provide instructions for checking their lengths during assembly. Making things more foolproof doesn't stop every fool, but it helps.
But I digress. The answer to your question is turn the motor one complete revolution and try again.
Also make sure your key is on, and your run/stop switch (on the handlebar is on). The latter being another common reason for the LED not coming on.




