Oh, geez. After some really precise checking, I actually don't think it's an inconsistency in where the timer starts upon starting versus restarting, but has to do with the invisible trigger that plays a spell sound. Because it creates a "textbox," it stops the timer for one frame the first time, but doesn't on subsequent attempts. No one would've ever noticed this if that hadn't happened to be a level with a guaranteed strat. I guess I'll have to manually make it so triggers like that never pause the timer.
Although even now that starting/restarting is consistent on that level, I think there's an inconsistency where the "new record" screen allows a slightly faster time...
Oh, and in the process, I tried making it so the girls call the "is level complete now" function upon exiting instead of having my main controller check that each frame, which shortens times slightly. Wondering if I should keep it that way.
EDIT: Fixed the time-improved screen issue by just adding an extra frame in that case to match the others. Now 5.45 should be the time every time. (I think my textbox fix may have also fixed jump inputs getting cancelled in 0-12?) And I'm keeping the direct calling of the level end check, which presumably takes a frame off every level.
EDIT 2: WAIT I BROKE LEVEL-FINISHING WHEN THERE ARE TWO OF YOU. Hold on while I fix that. Fixed that.