I am running quite a few P4's and dual Xeons all with Hyperthreading enabled. All machines are running JBoss 3.2.1, Sun JDK 1.4.2_02 and Red Hat Enterprise Linux and we have not had any of these issues. Hyperthreading has been a very small speed increase.
However, some colleages of mine who are running another application server on Windows 2000 are having a LOT of issues with Hyperthreading.
Thanks! Forgot to mention that this is also a Win2K box.