Good question, I haven't had one apart or to time one, have you timed it per the manual? I think there is a T that is suppose to be at the top from what I have read on here I think! Or I know it would some work take side cover off and put it at TDC and see where the mark are and then check compression then if it doesn't have any the something isn't right or it could be 180 off.
Just thought of something else, could the mark be lined up right but the cam be set wrong with the chain? so the valves would opening wrong but the marks on flywheel would show its timed right.