Did you do a default installation? My preferences.txt ended up in C:\Documents and Settings\Dave\Application Settings\Arduino(But I have no idea how it got there. I just unzipped arduino-0018.zip in a "sandbox" directory and started it up.)
This is better than nothing.
I'm not sure I'm entirely clear on the supposed bug here. If you quit (File > Quit or Control-Q), the IDE should save and restore the sketches you have open, along with their location and position.
My latest Teensyduino installer adds a patch for bug #78. Even if you never intend to use Teensy, you can run the installer on your Arduino 0021 and it should fix this, plus a few other long-standing bugs.http://www.pjrc.com/teensy/td_download.html
By the way, I take it that it'd difficult to make your own changes to the IDE?
If the installer worked, you'll see 4 new "Teensy" items in the Tools > Boards menu, and a couple new menus like Tools > USB Type.