Yes you can. I did it by accident actually because I was also having problems jailbreaking my 3gs 3.0.1. I finally ended up restoring mine to the updated version and was able to finally jailbreak it. What process were you using?
Downloading ipsw for 3.0.1. But I figured out you have to save the .zip file as a .ipsw file. That ended up doing the trick for me. Also I used the 3.0 ipsw restore instead of the 3.0.1.