Okay, once again. The "time left" values generated before reenabling the game time were not accurate, just estimated. They didn't count vacations, weekend days etc. That's why several games seemed to be timeouted but when a timeout occurs and the corresponding player has a day off (weekend, vacation, site holiday), the game is protected and the script adds 24 hours to its time left.
It's nothing but logical. The purpose of days off is to avoid timeouts. That's why no timeouts can happen during such days.