Was your top layer specified as a signal plane? If not, I suspect you simply picked the wrong file for that layer - one of the aux or stencil layer files, perhaps.
I’ve successfully had Osmond boards made by BatchPCB several times, although not recently. The only thing to watch out for (and this doesn’t apply only here) is to make sure that your design is entirely above and to the right of the origin: in other words, no points should have a zero or negative coordinate value. Osmond seems to do something funky with them, that looks right in some Gerber viewers, but has problems in others.
I’m using Osmond Quartz. What I mean with “very OS9”, is things like that it still clings very much to things like the creator-id. Which means that once you’ve edited a file, like a library, or so in TextEdit, it refuses to open it.
I’ve been playing with Eagle a bit, and I think I quite like that, the X11 interface notwithstanding.
But thanks for the offer to look at the files I might take you up on that if I decide to continue with Osmond.