Make sure the folder itself, outside of UTAU, has all of its files in the right hierarchy, and that you're pointing UTAU to the folder that contains all the suffix folders, rather than the folder that contains the folder that has all of the suffix folders. Example:
→Linako's Folder
→Linako Gentle (← you should be starting at this folder, not the one above.)
→A3
→C4
→E4
If you don't already, you might want to try pointing UTAU to the voicebank folder rather than putting the voicebank right in the "voice" folder.
To do this, go to Tools>Options and click the "Bank Regist." tab. Once there, press "Select..." and navigate to the Voice Bank's main hierarchy. Press the dropdown next to the filename (it should say "wav file") and change it so it says "all files" instead. Choose the any file in the main folder (eg, readme, character.txt, icon.bmp...) and press Open, then the "add" button.
The Voice Bank should now be in your drop down list, and working correctly with it's prefixes/suffixes.
Sounds like you should double check all your region and language settings then do a full re-install of UTAU (including getting rid of the weird second copy) if the problem persists.