Never under estimate the power of Google search it seems! 
I had a problem importing a new company logo into FCP which had a transparent background to it. I wasted serveral hours trying to sync it up with Motion to allow it to play the graphic on a seperate video channel WITH the transparency setting still working on it.
Low and behold I then realised that I hadn’t “googled it” so while in the horrible wasted time of “Rendering” I did just that and found exactly what I was looking for!
That helpful site “Creative cow” had a forum thread with the same problem and this was posted into it by a chap called Brandon Ivey -
“When you pull the PNG into your time line and it is not transparent, click on the clip and go to the modify option in your menu bar. There, go down to “alpha type” and choose “straight”. I dont know why you have to do it now, but thats what I found works.”
It worked a treat!! So thanks Brandon!