Ask yourself, who is really responsible for the error message? It looks like its some function called from DB_File.xs (actually db_open). So to figure out what the error means you need to learn as much as you can about BerkeleyDB's db_open.

A quick google for BerkeleyDB "Bad File Descriptor" yields an entry in http://www.sleepycat.com/xmldocs/ref/java/faq.html, which talks about it being an issue with large files, and that the solution is to upgrade (yes I know it talks about JNI, but you should try it anyway, as well as the --disable-largefile option).

What you should do is use db_verify and db_stat to learn as much as you can about your file, and then try upgrading/re-compiling your BerkeleyDB (and subsequently your DB_File) to see if that does anything.

My guess is that you'll probably have to contact the BerkeleyDB developers for help.