0.741 Patch:
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Version 0.74 is required, just download the patch and copy the contents over everything in your 0.74 folder.
I managed to get the Tower incident to repeat for me too. It was an issue where a "player paralyzing event" was running at the same time I had another event trying to make the player transparent. It couldn't do so, and was politely waiting for the paralyzing event to finish... which is never going to happen because it's a parallel event. >.>;
I fixed this by turning off the paralyzing switch before making the player transparent. I also moved the transparent thing to a better location, so Sienna should no longer be appearing and disappearing at strange times during those events. So the tower night events are fixed. Yay!
I also took a look at the potions event again. Honestly I just can't imagine what the cause is, BUT the time system has pussied up things before, so I think that is the same issue again here. You're probably reading the tonic selection dialogue and deciding on numbers while time is passing, which also causes other stuff to happen. This was especially notorious for messing up players trying to use doors (I've tried to fix all of those, but I'm sure I missed some.. doh! But I will get to them! Sometime...).
I "think" that I have fixed this as well. Potion making now disables time, but also uses up 10 minutes per potion made. This was originally intended but I forgot to add it in before releasing .74 (it's a new system, after all). There could also be similar issues with the water/cloth making station, transmuting, etc.. I'll try and get those fixed up for a future release, but if it's a big issue then let me know and I'll see about getting another patch out.
Please let me know if you still have any problems with either of these two events. Thanks for letting me know about the bugs!
Edit: Just musing, but I would surmise that most players aren't noticing these issues because they have played before and skip through most Tower scenes, and the potion making glitch would only be noticeable during a need or time fail (like the time going past 1080 as you are checking the potion making, and an animation plays letting you know Sienna is sleepy- and the game just borks out). Anyway I hope this fixes the issue for both of you. Thanks again for pointing out the bugs!