As mentioned previously, one of the Title Updates overrides the metadata changes that RB:HP makes to allow for 3-part harmonies, sending it back to solo vocals only.
We've already known that you could fiddle with the values in the songcache file via a hex editor to get the harmonies working again, but I've recently made it a little easier by creating a script to make this fix using my "CacheTools" utility.
Check out this thread for details. The "Proud Mary" script is already there in the zip download.
(NOTE: Alpha-release software! Use at your own risk!)