Hello. James from Futuremark here again.
We've confirmed that there was an issue with the GUI, and we're in the process of rolling out an update (3DMark v2.2.3509) that should fix the scoring discrepancy.
With this update, overall scores increase slightly by up to 0.3%. Scores from the Physics and CPU parts of benchmark tests may improve by up to 2.5%. These changes bring the scores from 3DMark v2.2.3509 back in line with results from earlier versions that did not have the GUI issue.
For context, it is normal for 3DMark scores to vary by up to 3% between runs since there are some factors in a modern, multitasking operating system that cannot be completely controlled. So again, all credit to @Papusan for noticing the problem and bringing it to us.
To get the update, just open 3DMark and you should get a notification with the option to install it. The Steam version and Steam demo have also been updated.