The .limewire folder is the preferences folder. There's no folder called 'preferences' inside it. You don't have to open it, just delete the whole .limewire folder. You might've deleted it before, it's a fix for quite a few problems. But after you deleted the folder, a new one would've been created the next time you started LW.

Same with the prefs folder in the new location, within Application Data. It's called LimeWire & you just delete the whole thing, no need to open it.