One thought is that your unprinted graphics need longer to resolve/cache to the iPad, which is a WAN connection.
FM Go's first version needed a scripted pause before prints were executed, however short. It may be that adding a scripted pause of a couple of seconds after switching to the print layout but before generating the output would allow these graphics to cache better.
Hmm, well we're using a local copy on the iPad so I don't think WAN would be the issue. But I'll try putting a pause in the script and see if that works.