All dialogue boxes and cutscenes will stop the in game timer. Pausing will also stop the IGT too. I would say the IGT isn't very reliable because it only ticks ups on the second. So any time you fade to black the timer will not count the remainder of that last second and will reset when the new scene initializes. If anyone is going to upload to speedrun.com, maybe RTA is the way to go?
I just had a look at the first bosses code and you're right, its not resetting the jump shot on hit. I'll have to release another update to fix that bug so it all works as intended in Bonus mode. It won't have any effect on the base game though so I won't worry about the update for a week or so (just so I don't keep flooding peoples feeds with updates every other day haha). But I do want to make sure the game is polished enough to work as intended for speedrunning so I'll definitely fix that up. Thanks for double checking!
Oh interesting! There did seem to be a big gap between RTA and IGT when my times were higher when checking the computer clock for time reference so that makes sense.
No problem on the updates, I’ll probably keep playing it over these next few days so I’ll make sure to let you know anything else I stumble across if you were looking to polish it up more.