Hi Jason,
Yes unfortunately that is a known issue with update action windows that is logged as Problem 5988. If you contact Support they can get the full details for you.
In regards to the way the calculations are written, my personal preference is your original layout. This keeps the decisions separate from the actual text it spits out so should be easier to read the values and logic. To get your SetHidden value set at the top how you want it would be using the same technique we already use - give it a default value and change it based on some decisions. Like this:
SetHidden = true if Request._NewUserFolderAccess != null and Request._NewUserFolderAccess == true: SetHidden = false SetMandatory = true .....