Mechanical timing

[osal]

I was checking if my cam timing was correct and after many revolutions i got the markings on the cam sprockets and chain to align at TDC as seen below.
http://i32.tinypic.com/4gjbir.jpg

However i noticed that the lower timing chain marks do not align with the yellow marking as seen below.
http://i27.tinypic.com/20tgzn9.jpg

I would have thought that since the timing on the upper chain is correct, the timing on the lower chain would be too. Is this true? or are they not related?
I did my search but could not really find the answer to this.

Thanks

[osal]

anybody?...
my car has been really slow yet it idles fine.

[importdude]

lower mark will not line up for X(not too sure) amount of times

[osal]

oh so if i just keep turning the engine, eventually both the upper and lower chains together will line up with their corresponding markings?

[JDS Performance]

I am not sure how many revolutions it will take to align them back up - but I do know its alot and not worth the trouble.

If you engine is out of time - it either
- will not start
- idle like crap
- bend the crap out of your valves