Same name, slightly different location. Your new folder is in My Documents, your previous Shared is in the 2nd previous higher up folder hierarchy. You should move them across, then press the Refresh button on LW. yes they both are called Shared, but in slightly different locations.

C:\Documents and Settings\your username\Shared -> C:\Documents & Settings\your username \My Documents\LimeWire\Shared

C:\Documents and Settings - your username - Shared
C:\Documents and Settings - your username - My Documents - LimeWire - Shared

See how there are a couple of levels between.