Hi,
So I am not able to reproduce the issue with the Team Competition mod; permanight is working for me with it.
However, as I've thought about it, I think this might arise from a combination of default settings and not understanding what's going on behind the scenes. By default, Clockwork makes days 4 times longer and starts in the morning. The grace period only pauses the clock; at the end of the grace period, time is not advanced to dusk immediately. This means the default Factorio day of about 7 minutes becomes 28 minutes, and thus with a 1 minute grace period, you can still be waiting around 20 minutes for night to fall.
To speed it along, you can change the start time to "0.0" (high noon), or a bit later such as "0.25" (start of dusk), and change the daylength multiplier to "1" or perhaps even a bit less.
If you're very sure it was a bug and not just waiting for the day to pass, then it would seem it's not Team Comp, or its some combination of non-default settings with Team Comp; either way, I'd need a save to troubleshoot further.
Thanks.