Microsoft Vista has secured the "c
rogram files" directory from applications. You can install into that directory with Admin privileges but running an app that needs to write data there will be a problem. Microsoft wants all of the data to be separated from the executables. This is a problem with Eclipse since it wants to write your preferences to configuration/.settings under the Eclipse Program Files install.
I ran into this on OS/X in which root installed Eclipse under /Applications and my regular user id had no access to write the setting out. But on OS/X it was a simple chmod to fix the issue.
On Vista, it appears that File Vitualization needs to be enabled. I'm in the process of testing this out and will post the needed steps shortly.
