You need to pay attention to whether the file was inserted with the "store by reference" option or not. Store by Reference PDF's can be opened by double clicking the file or via a go to field script step with the select/perform option specified. PDF's that were not inserted with this option must be exported in order to open them. The export Field option in the edit menu and it's matching script step will do that for you.
Export Field Contents also opens "by reference" files so this can be a good "one size fits all" option, but be careful. If the user intends to open the PDF, add comments to it and then close the file, files opened with Export Field Contents are copies of the original and arent' automatically saved back into the container field. With this option, they, or a script would need to re-insert the file into the original container field or the next person to open the PDF will not see the added comments.
Thanks for your help. I eventually used SuperContainer and it works really well. The FileMaker only way seems a little "cluncky".