Hey thanks for the high praise! I really appreciate it! And thanks for playing!
Basically bugs should be expected at any point in your game if you have used the computers. They're to mess around with the game but in a game breaking way. If you start a fresh playthrough from the beginning and you still find this issue it could be something for me to look into but what you are describing doesn't seem possible without using the computers. That variable definitely gets cleared. I will comb through the code though. Do you have a digital or physical copy?
If you found the secret room it is stored across playthroughs so that you can easily access it. I did that intentionally so that if you wanted to use the computers you wouldn't have to go through that process every time.