Capture feature in the GUI is sometimes wildly inconsistent

[PetrutDamian]

While testing the capture feature with a ~1 minute capture duration I sometimes get files with thousands more frames logged.
Tested the capture in Total War: Shogun 2, using DX11, in fullscreen mode, in a replay after map loaded standing still in the same spot each time. During the test I get about 50-60 fps with no visible artifacts or any sort of issues. However here are some csv stat results that I gathered in order:

Out of 4 sample runs only the first one resembles a correct capture. The rest gave wildly off numbers that I can't make sense of. This issue isn't a one off and happened after rebooting the system. I have also noticed this behavior while testing Age of Empires 2 Definitive Edition using the built-in benchmark tool but in that case it seemed to work properly more often than not. I have attached some samples of the actual frame capture files.

good_pass.csv

bad_pass.csv

Notably, at line 359 there is a frame which allegedly took 50seconds to render which definitely didn't happend during game. Present mode is also "Composed: Flip" at this time, which I am unsure what it means here as I was running in Full Screen the entire time. The good pass only has Hardware independent flip.

bad_pass2.csv

EDIT: It seems that if I restart(close and reopen) Intel PresentMon every time before capturing it works the way I expect it and gives data similar to the one in good_pass file.