whenever I load it. The options and read-only are checked, and updating them seems to fix it (un/rechecking). This may be related to Newlines are replaced by spaces, as they both happen when loading the project and can be temporarily fixed by updating the value
Aha, I found out the problem! This only happens when you have a block with a lone percent sign and a dropdown menu in it. Then it would be more similar to this bug.
Thanks for tracking this down. The use of in-band signalling (text characters with special meanings) in blockspecs is imho one of the unfortunate things we inherited from Scratch.