I'm logging this here because I haven't found a solution to it yet; I'll add one if/when I do.

My installation of Oxygen which has been working fine for a couple of years, currently at 15.2. I use XEP a lot. Recently I updated the OS (from Ubuntu 12.04 to 14.04, both 64-bit), which may or may not be the cause of the problem, which is this:

When I run a transformation scenario which does XML-XSLT-XSLFO-PDF using XEP, I get this error:

invalid file (bad magic number): Exec format error

However, when I run the same process on the command line, starting with the FO file, it works fine. The XEP license file and xep.xml file are in place, and haven't been changed. Even if I run the process pointing explicitly at the /bin/java in the Oxygen JRE folder, it still works fine, so it's not a problem with Oxygen's Java being different from my system default (which is OpenJDK-7, as it has been for a long time).