Azrend

I was opening a project that I had copied (using "save copy as"). I played it back, but I noticed that some notes were not synchronized to when I had placed them. The lead instrument, for example, would start playing early, even though the placement of the note is where I want it to be. However, everything sounds fine when I export it. It sounded fine when I saved it, so why did it get messed up when I opened it?