Great finding!
As to why does it happen - I don't know, for now it's certainly not frame counter overflow, physics always run at 60Hz.
7m 9.7s would be about 25782 +- 6 frames, nowhere around int16 limit

I'll try to measure that on my PC, as I have 100Hz monitor, if that was related to v-sync then I should get freeze earlier.

It's not v-sync related, always 7m 9s independent from the frame rate, it seems the freeze happens everywhere, in game and in the menu, so something global is causing it.

Freeze lasts for 0.500ms, +-40ms (I know, I should've enabled 3 decimal places, not two)
I have counted 7m 9s 500ms +-40ms, still correct with your measurements in the margin of error

And it seems it's 7m9s between freezes even if you turn off the game completely and turn it on later, might be some Windows stuff

That's also something I noticed in lots of people's videos and what always kept me wondering what's wrong with their configuration, because I don't remember ever experiencing it, at least not regularly.

I think it's not a good idea to assume this happens consistently regardless of the hardware and software configuration. That factor must be taken into consideration.

Most of people seem to be running on Windows 10 + ??? hardware, which means that we need a bigger sample of players running on other operating systems, including Linux and Mac if possible.

As for myself, I run Windows 8.1 x64 Basic Edition on an Asus X555LJ notebook and don't experience the same issue (see my videos). Additionally, I run the game using the Glide renderer, through nGlide software wrapper.

These things might be all very important, because if one mode behaves consistently differently, we might need to enforce that everyone uses the same config.

Yeah, after testing I couldn't get this freeze on Windows 7 (even with StuntKit skScreen)
On WIn10 I get freezes on D3D and Glide versions (through nGlide)
It is synchronised with Windows uptime (freeze at 07:09, 14:18 and 21:28) (give or take few seconds)

Didn't help:
• Disabling Windows Defender
• Windows 98 compatibility mode

I should've posted this here earlier, skFreeze is allowed, and it fixes the issue: https://github.com/Halamix2/StuntKit_modules