It's nice that you want to
"Help us improve the Arduino software, . . ."
You must be wondering if you and macegr are the only one's with this problem. :o
It's gotten pretty simple to reproduce:
1. edit a sketch
2. either close with the X
or just open a new sketch
3. you are prompted if you want to save your work - hit "Yes"
4. you loose your work
This happens on Windows (at least).
Well, just sit tight and keep pressing that save arrow! The doctor will be with you soon.
OK I admit this is pretty flip. But having a bug in an IDE that causes developers to loose their work is about as bad a bug as you can have (IMO). If I were a principal here, after verifying the bug, I would make a post to warn others. That's really my only goal here.