I just came across this same issue. How the issue was created was that I copied an SSIS package and renamed it BEFORE bringing it into BIDS. Doing that I was not able to change the scope of the existing variables to reflect the new name of the SSIS package.

After reading this thread I decided to bring in the copied package (with no name change) into BIDS. I then renamed the package within BIDS. After doing so the scope now picked up the newly named package. In the properties window it was immediate but I needed to close the package and reopen for the scope of the variable to be reflected in the variable window.

Hope that helps.