SWFs broken in Presenter

I'm having a number of problems with SWFs in Presenter.

In a couple of cases the SWFs don't stop on the first frame of the timeline as they should.

Movie clip button doesn't stop at first frame as it should.

The SWF background color becomes transparent so slide background shows through

Scrollpane components are cropped showing only a portion of the contents

Some transparent objects (alpha = 0) are visible i.e. solid color.