Is no-one else seeing this? I have just updated my 3.0 3GS to 3.1.2 using iTunes having never jailbroken or unlocked and with official SIM. Everything done with Apple's stuff their recommended way. I used the opportuntiy to grab my iBEC and iBSS as well as ECID/SHSH but didn't do anything unofficial to the phone.

Now it is slow as hell. The update mentioned fixing the wake-up slowness bug that happened occasionally on 3.0, but now it is much more frequent and many times worse. The whole UI lags - the unlock slide, wake-up, keyboard, starting an app or going home. We're talking whole seconds here, not small delays. It seems a bit intermittent - was fine for most of this post but now keyboard lagging like hell. Reboot fixes for a while but then starts again. Almost as if something in background is hogging CPU. Any ideas?

A full reset (home & power) of the phone took a long time to restart, and then seemed to have cleared things up. However, eventually it started acting slow again (although not as bad most of the time, still very obvious on unlocking screen etc.). It might have been triggered by joining a wifi network. Is no one else seeing this extreme slowness on stock 3.1.2? I'm thinking it could be related to the wifi issues.

Have you tried a restore and then setting the iPhone up as a new phone rather than reloading the backup that iTunes saves each time you sync your iPhone?

Warning, you will lose SMS, call history and application settings if you do this.

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

Nope, not yet. Primarily because I don't want to lose those things. I've heard that you can restore as new phone THEN restore from backup and that can still help, but I don't really see how, since any dodgy backed-up settings would also be restored presumably. Any idea?

If you are careful you can take a copy of the current iTunes backup for your iPhone then set the iPhone up as new and if it does not work then you can copy into the correct directory your backup of the backup and restore this to your iPhone.

That allows you to test the iPhone as new and if that does not help revert back to what you had before (any call or sms history that occurs while you are testing the "as new" will be lost, there is no way to merge this into your existing backup)

Also, the backup consists of a series of individual files, so it might be possible to identify the problematic (crap) bits and remove these, but still restore the important stuff.

Both of these things do not require a jailbreak, just carefully taking a copy of the iTunes backup for your iPhone and lots of testing.

Also, if your backup is encrypted, you can't do the things I suggested.

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

No, not encrypted. I always a bit cautious about iTunes removing its own backups, so that's what I would have done.

I think I'll wait to see if more people have this problem first, quite surprised that they haven't since I've never had settings issues before. Testing will take several days, losing SMS/history data that won't be in the backup.

Have you seen this specific problem with other firmwares or misconfigured phones or just guessing at catch-all fix?

I have only ever experienced keyboard lag, where the keyboard input lags behind what you type. Older OS versions had performance problems opening some apps SMS and Settings especially.
Apple tests the restore from itunes backup and tries to make it work well (outside of backup) so I am unsure if this will fix your problem. However the set up iPhone as new is a great catch all solution.

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

Sorry, my point was more that if I want to keep settings etc. then restore as new may fix the problem then restore backup would reinstate it, right?

This problem appears to only happen with wifi. If I reboot with wifi off, the phone does not seem to become slow. I think my home network is also OK, but not 100% sure. When I get to work, it goes slow.

It seems to also cause issues switching data connection type - GPRS -> 3G or the other way destroys the connection. If I've been out of signal, and go back to 3G (e.g. inside a building) I lose the data connection still for ages. Quickest thing is switch to airplane mode and back. I'm thinking a reset network settings is the first choice, although of course I lose all the wifi p/w details for friends' houses etc. :S