You are certainly introducing errors into your cuts by your method of measuring, as has been said.
I have a simple method for setting up for repeat cuts on my MFT, relative to the flag stop, more so if I have to return later to cut more of the same.
I cut a strip, usually a piece of 18mm ply about 25mm wide (not essential) which I measure, mark & then cut on the MFT, with the flag stop set,
to get to the required length, may take a couple of cuts and marginal movement of the stop to sneak up on it, this then doesn't rely on the splinter guard position, once I have my precise length I fix with a couple of screws a short back stop (off cut from the 18mm ply strip) on top of the cut ply strip, set tight up against the back edge of the guide rail, with the cut strip still referencing to the flag stop, I can then put it aside for
reuse later, with no need to measure again, I keep all them until the project is finished.