Not having the ASCII-85 filter in place is perfectly legal for a PDF. I wonder why you need that filter so your process works. Either you're working with a bad PDF viewer/reader or you're doing something wrong in stream handling, for example using Readers and Writers instead of InputStreams and OutputStreams. PDF is binary!
Jeremias,
Thank you! After going back deep into our code, we found that we were in fact using an InputStreamReader along the way. Right now we replaced everything with binary for FOP, and it works like a charm. I did also notice that the deflate filter is not applied to JPEG which is a good thing since they are already compressed.
Yakov
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