Quote from agrif
I ran into this problem the other day as well. It seems to only happen with the 1.9pre jar.
Anyway, I've fixed the code and uploaded a 1.9pre2-compatible jar here. Please, check it out and make sure it works for you.
(Edit: My first updated version broke the GUI, so I re-fixed that. I've also updated my first post with the new link.)
Seems to work fine, did a test render from scratch and the color gradations are there. This is very good news because people who tried the 1.9 pre-release would wind up with hung BiomeExtractor processes eating 100% CPU, and I've been having to go through and find/kill those by hand since we do map updates twice a day.
Also, someone asked how you load both the client and server jars from the command line in Linux but I think they deleted their post. In case anyone needs to know, this is how you do it:
java -jar BiomeExtractor.jar -jar /path/to/minecraft_server.jar -nogui world/
It will look in ~/.minecraft/bin to find the client minecraft.jar, so you don't have to specify it on the commandline, but make sure it's there.