timing chain- paint marks

[tmontague]

while checking my valve clearance the other day I noticed that when I had set the engine up in TDC with the marks on each cam shaft gear facing the 12:00 position and the drive shaft mark facing the "0" point the paint marks (orange links) on the chain were not lined up with these points.

I am wondering if this means that the chain just wasn't installed with the colored links on the proper position or do these links only line up perfectly every certain rotation of the crank shaft? I assumed that these marks would line up as soon as the crank shaft was in TDC. I know that I had TDC set up properly based on the position of the three marks and positioning of the cams when checking them, however I am wondering how you get the marked links to line up with these 3 points as well