Turns out it’s a common problem when dual-booting Windows and Linux, they keep changing the hardware system clock on each other (unless you live in GMT+0 zone) because Windows assume the system time is the one at the set timezone while Linux think the system time is the UTC+0 time (and offset it afterwards).

Linux updates the time through NTP server blindly while Windows 7 check if the current time is within 1hr from the NTP server to avoid unintended time changes (I have to give Microsoft credit for that). EDIT: Windows 10 blindly updates the time like Linux too.

The easy solution is to have Linux follow Windows’ suit:

timedatectl set-local-rtc 1 --adjust-system-clock