The outcome from my report to Tech Support was that transparency in flash items is not supported for mouse over events. Given that a significant use of flash is some sort of mouse interaction this is not very useful.
In earlier versions of Inspire you could have a transparent background for say the interactive stopwatch and it still work - so it's a shame this functionality has been reduced in more recent builds of inspire.
My advise to fellow users would be to leave the flash transparency at the default false setting.