Changed timing chain then turned it over manually now out of line

I placed the timing chains on and they were all lined up with the markings. We turned the motor over clockwise to make sure all of the tensioners were working properly and it wasn’t jumping a tooth. After turning it over numerous times trying to line up the time marks again on the camshafts. I was finally able to line them back up as they were when I put them on; however the main bottom chain is not lined up with the markings on the crankshaft or the sprockets. So how did it start out all lined up starting in the nine o’clock position just how the manual shows and now they all won’t line back up together?