When I try to download the new version of Toribash, my Anti-Virus software keeps going crazy over it. And when I went to the installation, it exited out and said "Malware Detected!" Does 4.31 really have Malware?

Nope. Just set it to trusted via your anti-virus software and it should be fine.

As long as your copy of the installation is downloaded from toribash.com, it's guaranteed to be malware-free.