Found this on the Quicken support site. Seems like the issues may have to do with permissions:
Quicken 2007 Quicken 2007 has been tested with Microsoft® Windows® Vista, and no known issues exist in the most current release.
Quicken 2005 and 2006 Quicken 2006 and 2005 have been tested on Windows Vista, and the following issues have been identified:
a.. When accessing QHI help while running Windows Vista, an error message appears. There is no workaround for this issue. b.. If you have not upgraded to the latest release of each Quicken version, scripting errors occur when you access help topics. Update your version of Quicken to the latest release to resolve this issue. c.. If you are not logged in as an administrator, an error occurs when you try to update your version of Quicken. To resolve this issue, log in as an administrator and follow the update instructions for Quicken 2006 or Quicken
2005, depending on the version you are using. Quicken 2004 and earlier Quicken 2004 and earlier have not been fully tested on Windows Vista. Therefore, Intuit cannot guarantee Quicken functionality or offer technical support if you are using Windows Vista with these products. Quicken may or may not work properly on this operating system. If you are experiencing issues using Quicken on Windows Vista, you can install your current version of Quicken on a supported operating system or upgrade to the latest version of Quicken.