I recently had the engine apart, and I put it back together getting the timing precise. After driving around fine, I was checking a part on the engine, and I noticed there was oil seeping through the very bottom of the timing cover to redo the seal. When I took off the cam cover first, I rotated the crank, so that the cams would line up to their top with the pistons. However I noticed that the chain was 2-3 teeth ahead of the timing marks on the cams. When I removed the timing cover, I noticed the chain was 2-3 teeth ahead of the timing mark on the crank too. The chain had somehow completely jumped 2-3 teeth on every gear, but it was evenly done, so the engine ran fine. Could that be from when I installed the tensioner, and I rotated the crank back a bit to release the tensioner into the chain? I don't think the chain could be stretched, but could that be the case since my timing was off last time, and the pistons hit the valves? But even if the chain was stretched, how would the whole chain move forward over every single gear like that?
The painted links will only be on their marks one out of every nine times you see them. Don't sweat it. See this thread if curious why.
