I have installed CentOS 5.3 twice on the same machine using a USB flash drive with the net install files on it. Both times the http install goes well, but when I try to boot without the USB drive, the machine won't boot. It will only boot with the USB drive inserted. instead of the files for net install, the USB drive now has a syslinux directory.

I had thought that I took care to only install on the machine's hard drive. Is there a way to rescue this install? I don't know what i did wrong on install to have this happen. Obviously, this doesn't happen when installing from CD. I'm a developer and don't have guru level knowledge of Linux install issues.

Sounds like the bootloader is on the internal disk MBR, but it looks for the stage files on the USB.
Are you just looking to fix this (one time), or a general solution for net installs ?.

It would be nice to figure out why the installer did that, but the most important thing is to get the machine up and running. So If there is a way to move that directory off the USB and have it work or some other solution that's fine. It's a Varari rack server that I will be using for dev work. It doesn't yet have an optical drive so I thought the USB stick would be just as good.

Go get the bootinfoscript off sf.net and run that. Post the RESULT.txt it produces.
Simplest way to find out where everything is.