This
did not work for me. I got failure errors.
Manually compiling GD and then re-compiling Apache would get rid of the error but I never got the graphics on the "Show Current Disk Usage" page. All I got was the tables and data but the graphics had the white square with the red X on them.

Very frustating.
Anyway:
CentOS 3.5
Part of the problem was I had no idea I was either missing the gd-2.0.33 libraries or they were corrupt or something.

I had to manually install this.
gd is different from GD! 
I did not know that.
Install the gd libraries:
Code:
cd /root
wget http://www.boutell.com/gd/http/gd-2.0.33.tar.gz
cd gd-2.0.33
./configure
make
make install
Then install GD:
Code:
wget http://cpan.mirror.solnet.ch/modules/by-module/GD/GD-2.30.tar.gz
zcat GD-2.30.tar.gz | tar xvf -
cd GD-2.30
perl Makefile.PL
make
make install
(btw, it also worked with GD-2.19)
I didn't have to recompile Apache or anything. Possibly because I had already compiled with GD? My graphics show up now when running System Health --> Show Current Disk Usage!
I hope this helps at least one person because I had almost given up on fixing this.
Thanks all who have contributed up to this point and please let me know if there is a potential problem with what I've just done.

I hope cpanel update doesn't break this.
Thanks,
-Stinky