Basically I'm in the same boat, and I have not installed RemoteBuddy at all (though I probably will soon, as I use Plex, Hulu Desktop, etc.)

I have a unibody Macbook running a clean install of Lion (32-bit kernel), and the DS3 pairs easily after connecting the USB cable, pressing the PS button, and disconnecting the cable. But on the mini (64-bit kernel) I get the pairing passcode prompt. So it's a driver issue, either by virtue of 32 vs. 64-bit mode or the chipset difference. Shame really. Between bugs in Lion and new hardware quirks like this, it's a big step backwards from the "just works" I'm used to.

If anyone is able to reliably pair a DualShock 3 with the new Lion-standard Macs, please enlighten us!