I am running ME v3.9a but had this same problem in the previous version I was running, although now I couldn't tell you what version was. The problem is that prompt windows do not resize properly. Most recently, I was working with Variable Set String and if I enter enough text that the prompt displays two lines, then the bottom of the window chops the OK and Cancel buttons in half. I noticed that the window appears properly when I click the Set Manually button to position the window but still displays wrong when I run the macro. I've attached a couple pics for clarification. Notice one has the Commands window in the background. This is what displays when I click the Set Manually button. The other pic is what displays when the macro is run. I've had this issue with Text Box Display, Variable Set String - Prompt for Value and If Message.
Am I doing something wrong or missing something? Any help will be greatly appreciated.