It's not actually skipping any lines (I don't think), but I do know why it's happening.
Viewing post in Can you be Hypnotized by an Anime Girl? comments
I read through the script to see what is actually happening and found out the bug - total 2 removes 'standstart' from the list without actually running it, however since 'standstart' is now not in the list 'standstuff' is added to the list on total 3 without actually giving the player the stand up command, same thing happens after 'standstuff' is finished - on the next total 'standstart' is still not in the list so 'standstuff' is added again. To fix this I'd suggest adding 'standstuff' to the list while running the 'standstart' instead of checking the list at the begining of every total.
Apologies for the long comment and reading the game code and thank you for making such an amazing game and for responding to all the comments. <3