Adobe have just blogged this "ColdFusion Builder 3 Mandatory Update Release". This fixes issue 3761655 (Unable to Update Software)... although that ticket is still marked "to fix" not "fixed".
The issue was that the Help > Check of Updates option errored out with a 404. A bit of a schoolboy error which clearly demonstrates a lack of testing on Adobe's part (or the prerelease's...), but at least it's fixed now.
The pleasing thing about this fix is that not only have Adobe issued a fix, for one they've also actually repackaged the download, so new CFB3.0 users will already be patched. This is in contrast to ColdFusion, which has always stuck with the original download, and then requires one to install the updates after installation.
Hopefully this new approach will be applied to ColdFusion too.