Creaking noise from Drivetrain - Alignment Problem?
 

I have a strange problem that I’ve spent hours working on.
A couple of weeks ago a noticed something was not right in my drive train system when riding. I felt a grinding and popping from the drive train system.
I checked my chain wear and bottom bracket. The chain was worn and the bottom bracket felt “unsmooth”. So I replaced chain (same part number) and Bottom Bracket (different part number).
But I keep hearing creaking noise when peddling medium to hard and which only occurs in the middle chain ring in all rear gears. Other two chain rings work fine. Shifting works fine in all gears and chain rings.
I did notice that the rear derailleur jockey guide is jumping when the creaking sounds is made. It looks like where the chain is entering is not completely centered.
Is it possible the derailleur is bent, though I’m not sure how this could have occurred and it looks fine. The sound could be the same as I was hearing even before I replaced the parts.
I’ve already disassembled / reassembled the bottom bracket several times (greased, checked the spacers to make sure the chainline spacing is correct). So I don’t think this is the problem.
Could this be caused by a worn out middle chain ring? The teeth don’t look that bad to me.
Any other ideas?

Specs: Shimano M543 Crank Hollowtech II, Triple w/ 9 speed. Deore LX rear Derailleur.

It sounds like you have a worn out cassette.

When your chain was bad it was also wearing on the teeth of the cogs/chainrings. This changes the "spacing" between each tooth as well as the profile of the tooth (shark toothed). When you put on a new chain it won't fit the "redesigned" gear teeth any more.

You see one sign of this by the derailluer cage "jumping" as you put it. If you look closely at the chain as it wraps around the gear cluster you'll see it is lifting out of the tooth-pocket and riding on the tips of the teeth when the cage moves. When the chain can fit between the teeth again it falls into place, the cage jumps and the cycle starts over once more. This is called "skipping" and it can happen on both the rear cogs and the front chainwheels.

After thinking about it it more, it's logical that my middle chainring is worn out. So I ordered a replacement and will install it. If it doesn't work, I'll move to the rear cassette. I'll update here with the results.

If your chain is significantly worn, you should always replace your cassette as well.

You can get more life out of cassettes by using two chains and swapping them every 1000km or so.

I installed a new middle chain ring this weekend and I'm happy to report that all is well and the creaking in now gone!
I noticed that my chain wear went from within range to worn out pretty fast. I will now check more often especially when the chain starts to reach the end of life mileage.