Well, it seems that my configuration is confusing the tools. The 1.3.1 install that Eclipse was moaning about was from an installation of Oracle Tools (something I did over a year ago) - it seems that Oracle buries a JRE in there. So, I grabbed the latest 1.5 from Sun and installed that. It complained about installing files as it got close to finishing (apparently, I should have quit Firefox before starting). The upshot? I ended up with a corrupt set of files. So, I blew those away and have started installing the 1.5 files again.
Meanwhile, NetBeans seems to be fixated on an older rev that I blew away, and won't start or uninstall. That's lovely - highly friendly, that. IntelliJ collapsed after I uninstalled the version of the JDK I told it I had - it's idea of informing me there's a problem is a modal dialog with one button that pops up over and over again. Not impressed with that either. So, I think I'll have to just delete NetBeans and IntelliJ, and start the installs over.
All this just to look at tools that supposedly have great features I need to borrow from :)
Update: Ok, I removed all the old JRE and JDK stuff from the system, grabbed the 1.5 stuff from JavaSoft, installed, and dutifully rebooted Windows. Then I unzipped the Eclipse files again, and tried that. No dice - as it's trying to set up a workspace, it tosses an exception - java.lang.ExceptionInitializerError. Even better, eclipse is still running, as is the JVM it started. I couldn't delete the offending directory until I killed both. Restarting eclipse led to the same error.
I don't think "simple" describes what I'm seeing. There are words that do describe it, but they aren't family friendly...