Hi. That's odd. Every room should have a variable that defines the clone detonation time for that room. Also, some rooms have a more limited timer, and some puzzles works more like a speed challenge. If this was a glitch (It's also possible) maybe a room was left without that variable (and this made the game loads the last visited room value), you can try returning to 'level select hub'. There is a portal that makes you continue playing the last visited room (next to the Patriarch portal that transports players to that pyramid man). If this is a variable problem this should reset the timer to it's original value.
Also, there is an alternative to slow time on options, this enables the reset button to work as an on/off slow-motion (reset still working when the button is held).
I'm going to check the game again and look for left values, and thanks for playing :D