Your comments

Hey Tom, thanks for the explanation. I was actually able to get JPEG2000 support to work with your advice!  I added jai_imageio.jar file to Ubooquity.jar, and with the -Dorg.jpedal.jai=true parameter, JPEG2000 images inside pdfs are read perfectly.

I was also seeing another funny error in my logs:

java.lang.RuntimeException: This PDF file is encrypted and JPedal needs an additional library to
decode on the classpath (we recommend bouncycastle library).
There is additional explanation at http://www.idrsolutions.com/additional-jars
at org.jpedal.io.PdfFileReader.setupDecryption(Unknown Source) ~[jpedal_lgpl.jar.7484534240993843609.tmp:4.92b23]
at org.jpedal.io.PdfFileReader.readLegacyReferenceTable(Unknown Source) ~[jpedal_lgpl.jar.7484534240993843609.tmp:4.92b23]
at org.jpedal.io.PdfFileReader.readReferenceTable(Unknown Source) ~[jpedal_lgpl.jar.7484534240993843609.tmp:4.92b23]
at org.jpedal.PdfDecoder.openPdfFile(Unknown Source) ~[jpedal_lgpl.jar.7484534240993843609.tmp:4.92b23]
at org.jpedal.PdfDecoder.openPdfFile(Unknown Source) ~[jpedal_lgpl.jar.7484534240993843609.tmp:4.92b23]
at com.ubooquity.fileformat.pdf.c.a(SourceFile:37) ~[Ubooquity.jar:1.6.0]
at com.ubooquity.data.feeder.a.b(SourceFile:359) [Ubooquity.jar:1.6.0]
at com.ubooquity.data.feeder.a.a(SourceFile:202) [Ubooquity.jar:1.6.0]
at com.ubooquity.data.feeder.a.b(SourceFile:302) [Ubooquity.jar:1.6.0]
at com.ubooquity.data.feeder.a.a(SourceFile:34) [Ubooquity.jar:1.6.0]
at com.ubooquity.data.feeder.a$1.run(SourceFile:112) [Ubooquity.jar:1.6.0]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_65]

I don't have any password protected PDFs, but it does look like there is some encryption in my pdfs.  In any case, I did the same thing with the bouncycastle library as i did with jai: I added bcprov.jar to Ubooquity.jar, and voila my encrypted PDFs were read transparently by Ubooquity.

You might want to consider adding these two jars (and the -D flag) to Ubooquity, as it seems like it give Ubooquity additional features right out of the box.  I think pretty much all the crazy pdfs I throw at Ubooquity now work (I'll let you know if I find any other weird things).