My guess is u r inserting the PDF in a manner that doesn't mark the file as being a PDF.
I'm not sure why the container fields don't use the same logic as Mac OS (file extensions are the driver in determining which is the default app and which apps support the file type) but they don't. There is some other place where , on import / insert / set field a meta tag or flag is being set which tells filemaker how to handle the file. I have to deal with this all the time with image files. If u are using insert file, that will result in the file being stored as a file with no other handling instructions. It's actually very useful if u want to see the files listed out instead of seeing their content displayed.
Try this - manually drag the PDF that isn't working for u when u import , into a container and see if it displays properly then. By this I mean drag the original PDF file prior to being imported (where it is likely being marked up and is no longer a "clean PDF"). If it displays fine then my hunch is right. From there experiment with getting the file into the container using a different script step and/or calc.
I don't do much with pdfs but is there an insert PDF script step ? There is also a get as PDF calc as I recall ?
This might help the file get the proper tagging prior to being inserted into a container.
Hopefully one of the wizards here can shine some specific knowledge as to what the engine does in these cases. I basically hit the roadblock u are hitting, and quickly built a workaround as opposed to taking the time to understand the exact issues.
In Layout mode.Select the container field, go to the inspector and under the data tab at the bottom click "interactive content" then "start playback automatically". That should fix it.