Good morning, Linky439!
Thank you so much for documenting this one with so much detail, as well as the letting me know that that variable "bombs_wait" was being saved. This was something I definitely overlooked, and I will remove that pronto from my save script! :D
Again, thank you so much for finding it! And thank you for doing some extra investigating with the save files.
I will get a fix out this weekend (most likely today) that will fix that issue as well as the variable being saved. I have a new build I was going to be uploading today anyway, but it won't be a problem to go ahead and get this fixed as well.
Thanks again!! :D
EDIT: I was able to get this bug fixed, along with a few other tweaks, and a new installer is now live! :)