Same for me. I used a Vista machine to jailbreak, then back to Mac. Correct, don't sync anything with the Windows PC and you should be fine.
when I start black rain and the phone goes to recovery mode the window computer tells me in itunes "itunes has detected an iphone in recovery mode. you must restore this iphone before it can be used with itunes"
For those of you using Vista, be sure to right click on blackra1n.exe and ensure that the box "run compatible with Windows XP" has been checked and "run as administrator" is checked. Do this prior to running blackra1n.
Plug in your device, update to the latest firmware (if you're not at 3.1.2), then close iTunes. Right click on Blackra1n.exe and choose to run as administrator. Click "make it rain". Your device will now go into recovery mode. Don't be alarmed, this is normal. If iTunes opens back up and gives you that error message (as quoted above), just click OK and then close iTunes. BlackRa1n should finish doing its thing and voila!, JB on 3.1.2.
Which will also update your baseband and will probably prevent you from unlocking in the future.... no thanks.
Yes, that will update the baseband and disable the unlock. I'm on AT&T through work, so that isn't a concern for me. Tethering is though, which is why I still have my iphone running 3.0.1. I've only updated my ipt2 to 3.1.2. Honestly, the new software has no features worth updating.