Java shouldnt cause this issue unless there is a Java Plugin/app on the page you are viewing. I did just remember something else that definitely caused this issue for me (and made Firefox pretty unusable and horrendously slow). That something is various themes for Firefox - most especially in my experience the Vista/Aero ones - but various others as well.
I think I had the most success with one of the Orbit themes and a couple others. The differences ranged from the browser being horrendously slow to do anything (load a page, display a page, switch tabs, etc) - to the browser's UI (and with some themes, OS/2's GUI) becoming unusable/unresponsive.
Another issue (with Flash) is often the version of the plugin you are using - or whether something else (or another instance of Flash) has the sound card locked when a sound playing flash file is loaded. I get temporary hangs in the GUI (when FF hangs), to "permanent" hangs in both).
I've found (just recently - after having previously restarted each time) that doing something to take focus away from FF usually works after a little bit of a delay (one that exceeds the setting in OS/) - most success with CTRL-ESC/ALT-ESC combinations.
My biggest issue was on some occassions, shutting down FF or PMw-Fx would hang it (any build since at least 2.0.01). I got tired of rebooting, so madly hit CTRL-ESC and/or ALT-ESC (first tries switching to the task switcher app - ie: "Window List" and the second tries switching to a different program). After waiting 5-20 seconds, OS/2 responds with an "unknown process #____" is not responding... (and invariably with JUST an "OK" button to kill it - no cancel button). Selecting OK kills the remnants of FF, frees its memory and all is good.
Anyway, if I remember the name of the utility (NICE maybe?), I'll let you know.
I'm hopeful for a Cairo based build of FF someday soon... I truly think a lot of the issues are with the screen rendering code...