Why is my chain so noisy after cleaning and lubricating? I have recently gotten into commuting to work with a road bike.  Once a month or so I will degrease, clean, and lubricate the chain.  I change through all the gears to distribute the lubricant and wipe any excess from the chain when I am done.

The problem is that for the first 2 or 3 hours of riding after cleaning the chain, my bike is constantly making clicking+creaking noises.  They sound similar to what one would hear if the bike was having trouble changing gears and seem to be coming from the area of the rear derailleur.  I can "feel" the noise in pedals also.  It seems to be most noticeable in certain gears on the rear derailleur (3, 5, and 6) but totally absent in others (such as 4).

After a couple hours of riding the noise goes away and the bike feels great.  What is going on here?
Likely some coarse particles get in between the chain elements and also between the parts of the derailleur and the star wheels. After you cycle for a while those particles either fall out or get crushed into finer particles and thus the noise goes away.