Try 3.2.2 and a different JDK. I'm using a Pentium III laptop, Slackware 9.1 (kernel 2.4.22) with IBM Java 2 1.4.1. No problems with the lsof and I'm doing a lot of redeployments while I clean up code. The system or JBoss hasn't been shutdown for a couple of days.
I tried IBM's JDK and got some strange classpath errors with JBoss. JRockit wouldn't even start up. I ended up going with Blackdown.
Switched to 3.2.2 and that seems to have worked. There are still open handles to deleted files, but there are far fewer now by about ten fold. It's even a little faster than 3.2.1 by 7% according to the timings on my automated regression tests.