Thanks, that was it. I can't believe I missed that. I recently rebuilt my computer and didn't realize iCloud was on. I usually disable it first thing.
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History restored randomly
I have the version from the website, not the store.
I have Cookie set to clear history and cookies when closing the browser. If I close and open the browser all history is cleared. If I check the history after the browser has been open a for a while(don't know exact amount of time) all history has been restored.
Cookies are not restored, only history.
Edit: I've tested it. It happens about 7 seconds after the browser has been open every time.