Might also need to run with admin rights.
Thanx for the help buddy but i would like to share something that i have solved the problem and iused blackra1n to kick my 3gs for normal booting and also jailbreaked it. and its working like a butter. Sharing this may be some of our other friends would get help by this to kick their 3gs out of recovery mode and also jailbreaked on 3.1.2. thanx buddy for all the support.
I am glad that you solved your problem so you might be able to helpme!
Indeed, Can you give some more information about how you did solve your problam after you had been stacked with the irecovery problem?
Thank you so much for this. After hours messing around with Libusb trying to get it to recognize my iphone in DFU mode, I just switched back to recovery mode and ran blackra1n. Voila! instant booting and jailbroken to boot!