Microsoft introduced a number of restrictions in Vista that makes it more difficult to save program settings and temporary files.
Applications can no longer write to the Program Files directory, but even worse; the common application data directories, like ProgramData and Users\Default are by default only accessible for writes by administrators and the first user that did the write. Sessions by other users only have read access. The same goes for registry access; the computer keys can not be written by everyone.
As long as it is OK to not share settings between user's you have one good option left; the user's appdata folder. If you do need to share data though - you need to set the access right of the folders you create in the "common" directories. This can currently be achieved e.g. by using a tool like SetACL, however as it has been made a required action now, it should be included in the installer - AND preferably also as VIs on the file and registry (for registry access) palettes.
LabVIEW 2009 introduced one of the tools required to handle the UAC changes - a VI to get the paths of system folders. It should also have a tool to grant access to some of those paths...