I've received the same warning while configuring aMule 2.0.3, the only difference is that I've Fedora Core 2 with gd-lib 2.0.21
I tried to add --with-gdlib-config=/usr/bin/gdlib-config to the configure options, but it did'nt remove the warning.
So I decided to ignore the warning and go on compiling aMule.
Now all seems to work properly, I'm also able to see the progress bars in amuleweb.