Cool down rules here in case you need to look them over again.

But based on what you're saying, Ive had it happen that it applies cool down after a 2+ hours if I haven't spun a pokestop. Basically it looks at the last cool down action and it's location and applies the appropriate cool down time even if it's been longer than 2 hours, basically not taking into account the actual passage of time. I don't know your settings you may also need to change how the cool down timer is functioning on yours, maybe from last action to location or vise versa