I had my 3GS jailbroken, so i waited for 3.1 jailbreak.
I tried it today but each time the .ipsw file didnt work - I only got 1604 error messages.

After some hours my only way was to to a regular 3.1 upgrade - with no jailbreak now.

I had Categories installed and the Apps i had categoriezed were hidden using SBsettings.

After upgrading to 3.1 most icons were missing, so I deleted them using iTunes and then reinstalled - so my bought Apps are ok now.

But I miss some of the Apps that are normally preinstalled on the iPhone.
I don't have Settings on my iPhone Screen now - even the iPhone Search doent find it anymore.
Can anybody give me a hint how I get my Settings App back to my iPhone Screen ??

If you upgraded a Jailbroken iPhone and are missing icons for apps you put in categories then go to SETTING then GENERAL then RESTRICTIONS enable the restrictions and then disable the restrictions and that should bring back your icons for your apps.

Regarding the 1604 error did you have the iPhone in DFU mode? The custom ipsw from pwnage tool needs to be loaded with the phone in recovery mode.

Or did you try and do an upgrade instead of a restore with custom ipsw? Upgrade is not supported only restore due to issues migrating cydia packages in an upgrade scenario.

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iPhone 3GS 32GB factory unlocked (3.1; Pwnagetool, Cydia, OpenSSH)
iPhone 8BG (3.1.2; Pwnagetool, Cydia, OpenSSH)