Yes, this was a pesky bug that I thought I had fixed a few versions back, but only finally fixed it for real with v1.6. Basically, what happens is that when you pull the lever to open the floodgates, it closes that door, due to a weird bug with the editor I used to modify the title screen (Hyrule Magic is absolute garbage...). The first time through, it's not a problem because the door is supposed to be closed, but if you don't finish the dungeon in a single playthrough and try to come back, the bug hits you. Simple fix, cheat code 7EF05181, save and quit should permanently fix the save file. Sorry about that!