Correction: Now that I've read the Modding Tutorial page, I now know why it looks like puzzles were being "removed". Apologies for the false bug report.
Got 1 more bug to report. The game's crashed on me a few times in the middle of my play sessions claiming that I've run out of puzzles, which is impossible now since the mod I've created and am using has 1800+ puzzles currently, and at most I go through 10-15 puzzles at a time. I'm sending images of the crash log here:
I like this game a lot and I think it has room for growth, so I'm planning to give it a proper review sometime next weekend.