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1) When holding Shift and clicking on a Guildhall, the upgrade window doesn't always open, even when the fifth level has been built. Through experimentation, I've found that if there are no resources available, the upgrade menu won't open. This isn't very convenient because it's not entirely clear how many resources are needed.
2) If you open the upgrade window and close it without making any changes, you won't be able to open it again on the same day (it just takes you to the guild when you hold Shift and click). Is this happening to everyone? If so, it seems like a bug, and I don't see any logic behind it.
P.S. It would be nice to add up-to-date information to the first post. I had to go through half the thread to find the message about holding Shift to upgrade :-)
Try hovering your mouse over the very top of the guild when entering it. There was a similar bug; maybe it hasn't been fixed yet.