Thanks for the screen-shots. This problem is a bug reported several months ago and fixed in 6.0.1. See this section of the 6.0.1 Release Notes:
- In some instances bringing up a Flex Alert or Dialog box while an HTML view is opened would cause the Alert or Dialog to stay hidden behind the view (i.e. the iFrame doesn't disappear temporarily as it should) which in turns blocks the UI because the user cannot click anywhere to continue.
Any action that brings up a small popup dialog would have the same problem when the HTML view is active.
Unfortunately there is no good work-around. In your case hitting enter would dismiss the hidden "Disconnect" confirmation dialog, using the default No option.
I think it works for "New Alarm Definition" because this popup is larger.