Well, I ended up solving one problem and introducing another.
The drive was set as boot (I forgot about Gparted, had it already) and it was flagged as boot in there. I then tried the install from start again, and it would not work. I then tried it on another computer, and bingo, works first time. I'm guessing for some reason, the computer I was using will not support booting from USB, even though the BIOS is set to boot, and it does try to read it as it comes up with an error saying it is unable to boot from drive. It baffles me.
But now I have introduced a new problem. I tried to boot Ubuntu 9.04 from USB as a test on the computer that was supporting my booting from USB, and I can't get past GDM. Was never an issue before when I had an ATI X300 installed, but now that I upgraded that machine to a 2900GT, it won't work. I'm hoping someone on ubuntuforums will be able to answer that one.
Thanks for the help everyone.