How are you using Inline::Java? Client/Server ? JNI? Shared JVM? Are you using it from a standalone Perl script? CGI script? mod_perl handler?
All of these things affect the way it will interact. I've found JNI to usually be the fastest, but it's a little tricky to get right under mod_perl.
Have you tried asking your question on the inline mailing list where the real gurus of Inline::Java hang out?
-- More people are killed every year by pigs than by sharks, which shows you how good we are at evaluating risk. -- Bruce Schneier
