I have been using your IDE for a couple of years and absolutely love it - thanks for a great piece of software!
I am using version 2.0.2 on Ubuntu 10.04 (Lucid Lynx). Something started happening a couple of weeks ago that has never happened before. It happened once 2 weeks ago, once last week, and it just happened again. The "it" is that the IDE completely vanishes in the blink of an eye. And it always happens while I am simply typing code into the editor window. One second I am typing away, then BAM! Nothing. Gone.
When I restart it, I have invariably lost some typing, and it always goes through the complete re-indexing process. I don't know if you have two different kinds of index processing, but it seems when I start the IDE under normal cirucmstances it is ready to go in a fairly short time. When this happens I have learned to go get a cup of coffee, because it's going to be awhile before the IDE is ready to use.
I looked in the system/log/threadDumps folder and the last log file was created several hours ago when I started the IDE.