Hi, sorry for the delayed response! Yes this is that very issue you thought it was. The current build in dev has the fix but owing to how much we're still fixing and adding, it's taking us a bit longer than we'd like.
In response to your curiosity, it is technically a save game glitch. The engine uses a sort of VM and the save files are more or less save stating the VM. There was a bug in the current release that corrupted a few of the core state flags. Sorry for the inconvenience, but as you seem to have found out hitting certain rooms will force a state correction.
We're glad you've been enjoying the experience in spite of the bugs and hope to have the patch out very soon!