I am running Tomcat bundled with Liferay5.2.3 and use Eclipse 3.5 (Galileo) as my IDE. I set up my Tomcat server in Eclipse as per this blog entry: http://www.jroller.com/h
Although I still don't know where/how Tomcat determines where the default temp directory should be, nor do I know why Eclipse sets it to something different, I have found out that you can set the temp directory via a VM argument when starting Tomcat in Eclipse:
-Djava.io.tmpdir="C:\Program Files\liferay-portal-5.2.3-tomcat-6.0\tomcat-6.0.18\temp"