Ah, yeah, "ambitious" is definitely the word when it comes to the flags. It's odd that you're getting that level of repetition though - I suspect something's gone wrong that's caused a knock-on effect.
If you like, you can email contact@spiderlilystudios.com with the "retrace.save" file you'll find in your install directory (usually C:/Users/[your name]/AppData/retrace) and I can attempt to repair the save file for you, otherwise, judicious use of "New Game" and the fast forward function may be in order. I'm really sorry about this! It's been a year and a half since release and I'm still finding new ways the variables can interact to break everything. Even so, I'm glad you're finding it interesting!