Again, WOW! I just tried this with every computer in my house. I tried 3 different computers all with Windows XP Pro SP3 (one was a DeLL), with all updates and also Windows 7, with all updates, and all worked!. lol Check to see if you have every update installed. For Windows XP, you'd have to goto there update website, (Start->Programs->Windows Update) not the update program. When you did a fresh install, did you install ANY programs whatsoever? Because if you didn't, then its GOT to be your computer is totally screwed up beyond repair and just throw it out the window. Seriously! lol
And heres something even crazier, if you have the time, you could try this. I had 'Ubuntu Linux' installed via Virtualbox. And you will never believe what just happened. I ran '360 Flash Tool' using 'WINE' and, you'll never believe this, IT WORKED!!! Is there even .NET in WINE!!! lmao I opened the original bin, clicked patch, set everything, saved it to a NEW file, and NO ERROR! Seriously? How messed up is that! So, somehow, it's got to be your computer! What I don't understand, is you tried multiple computers, and all wouldn't work. Now thats messed up! lol Ctrl+Alt+Del EVERY program, and see what happens, and I mean EVERY program! lol Try re-downloading the program. The MD5 should be: abdd3b0be7f6fa8cc6cbb2ade6bd551e

Something funky is definitely going on. I just installed Ubuntu Linux in a Virtual Machine and 360 Flash Tool crashed when I clicked patch. The MD5 matches.