First of all, thank you very much for playing!
And thank you very much for this detailed bug report, very appreciated!
It seems that the game start failing in some points after first complete run. Some global variables are storing things that weren't expected and persist between games. We are working on it right now, and we will upload the patch asap.
For now, try entering in the Windows Regedit console and delete the content at \HKEY_CURRENT_USER\Software\Sepia Games\You are GROUNDED! It will set the game as a fresh start and might fix some of the issues you faced, but you will also lose all settings and progress. This quickfix doesn´t affect to get alternate endings.
And for the cockroaches, one hint: There is a tricky one before the scene you mentioned, but does not affect to the third ending.