I get the same error when running the recompile script and the IDE is clean.
I'm using build 1.6.4-9.11.1.965. The default installed IDE setup doesn't look at the minecraft_server directory, that I can see. The minecraft project is clean.
Digging into the commands.py script, I see it building a temp file of the packages for the server compile command. It leaves out net.minecraft.client; which is understandable except for the part that minecraft_server\net\minecraft\block\Block.java (and a slew of other .java files) do this:
import net.minecraft.client.renderer.texture.IconRegister;
It is used in client only functions, so I'd expect a Side.CLIENT tag on the import.
Is this a bug in the decomp or something in the filter used by the python?