Hello Scott,
If I understand correctly, it sounds like you have mounted your flash drive on your Windows OS and are trying to install from there. While I think this should still work, I usually change the boot priority to the flash drive to do installations. Here are the steps I follow.
Power down your PC
Insert your flash drive with your bootable Linux image
Power on your PC
When your BIOS loading screen displays (this will usually display the name of your hardware's manufacturer) press the F2 key (sometimes DEL, but you should see a message at the bottom of the screen saying which one is required)
You should now be in your BIOS menu
Use the arrow keys to select your boot priority and make sure your flash drive has the first priority
Press escape, save the changes and reboot
You should now see the Ubuntu logo and a menu to install the new OS
Some helpful links:
Creating a bootable Ubuntu USB
http://www.ubuntu.com/download/desktop/create-a-usb-stick-on-windows
How to enter the BIOS menu
http://notebooks.com/2011/05/05/how-to-load-bios-and-change-boot-configuration/
Now if you change the boot priority in your BIOS and you get a black screen with a message saying something like "boot loader not found" or "kernel panic," then the problem is probably with your Ubuntu image (while uncommon, image downloads can become corrupted). I would try to download a new bootable image (
http://www.ubuntu.com/download/desktop) and reload it onto your flash drive with the instructions linked above.