The color scheme you see is the default after the update to a next major release (which you have just done) You can easily swap this back by selecting your preferred skin from the settings within ruTorrent:
You will need to adjust your alias.username files if you have several users on the server. They can continue to keep using their /torrents directories as their own rtorrent.rc files have not been modified, nor have the /home/username/torrents directories been altered. The only directory altered is the master account.
The is a lot more on this posted here:
You will want to focus on the section Now that you've updated - Here's some points
The fix for the additional users is fairly simple. You can do as you mentioned, simply adjust their configuration files to point the alias to the new menu item link. This is the fastest solution, next to altering their directories like that of the master account and then having users do a 'Save to...' on their torrents.
This is the simplest solution for now as it was stated this is the final directory structure for QuickBox... essentially marking how we create a users home directory as completed and future-proofed.
The reason the /torrents directory has been altered is due to the inclusion of Deluge, having both Deluge and ruTorrent files in the same directory was confusing and cumbersome to users that had both running in tandom.