I had basically the opposite experience with the LCD-3: bought a pair during pre-orders, liked them but didn't love them. Had them RMA'ed, liked them more but still didn't love them. Sold them. Missed them, and bought another RMA'ed pair from the first run. Totally love them now, and my other cans get less and less head time every day.
In the absence of anything remotely scientific to suggest driver failure over time, I have another possible explanation: pad wear. Many users (including myself) have found the LCD-3 to be incredibly sensitive to pad shape and fullness. Is it possible that your pads are compressing and thereby compromising sound quality? This might be the case if, for example, you store them on a solid headphone rack like one of those mannequin-type deals.
Just a thought.