1. Get rid of Ubuntu (su 'rm -rf /') 2. Get Scientific Linux 3. ??? 4. Profit!
In all honesty though I haven't a clue what's going on mate. I don't even know what USB Legacy or Windows Boot Mode even is. From a quick look around on the interwebs, I found people saying they had problems with this USB Legacy stuff and those problems went away when they removed all connected USB devices. If that doesn't help, maybe try (re)installing the latest BIOS of your computer?
What are the differences between Ubuntu and Scientific Linux?