Unfortunately I never got a clear answer as to why this was happening.
It seems the best way to reduce the risk of problems is to make sure all your settings match between PS and FCP.
so if your FCP project is say, DVCPRO HD 720p then your PS settings should be for DVCPRO HD 720p or 960×720 with 1.33 pixel aspect ratio.
Making sure the file settings are the same eliminates a lot of “unknown” problems that can occur.
In a few instances I was never able to get the .png to import correctly and had to import the .psd file.