I'd be interested to hear how you used your dial indicator. You cannot just "look for" the highest point of the piston, as it's nearly stopped for a few degrees at TDC
What you must do is use the indicator the same way as you would a piston stop.........that is, stop the piston at an arbitrary point BTDC, mark the damper, then stop the piston on the way down at the same height ATDC and make a second mark. Your true TDC is halfway between the marks
If you are simply looking for "highest point" with an indicator it could easily be "off" that far by your method.
Also, it just might be that the piston rocking a little in the bore will add a tiny amount of "Murphy" into the equation..............