I'm practicing all sigils run, and I got very frustrated by this bug. Even though I typed correct password of floor 6 (which, of course, I got from each of the star levels), the computer would reply "code incorrect", no matter how many times I type it. And the only way to fix this seems to get out of the nexus level and reload it (by getting into and then out of one of the puzzle levels, which are indeed far away from The Tower). I experienced this bug in two runs so far, which wasted a good deal of time. Has anyone experienced this? or anyone know what causes this bug?

Yes, that killed many runs before. I don't think a bug though. You can't type in the code without seeing it in the star worlds. And they mean that literally. It seems like there's a look trigger on those signs that 'unlocks' that part of the code. Make sure you look straight at the signs at least once when you're in the star worlds.