Okay, first, the Quest Rules pages that have 2 pages are messing up (Items, Enemies, and NES Fixes). If you go into the menu and then click ok (doesnt matter if you set anything or not), the other page will have all of its rules checked. (ie. If your on page 1 and click ok, page 2 is messed up, and if your on page 2 and click ok, page 2 gets messed up.)
Second, Screen Data kinda does the opposite. If you go in and set something and click ok, it saves it. But if you go back in, go to another page, and then click ok, all of the other pages checkboxes are reset to unchecked. (Only the checkboxes are affected though, pull-down menus and text boxes are not.)
Third, Dmap flag checkboxes has the same problem Screen Data does.
That's all of the dialog box issues I have found so far, and I think I have tested them all now.