Noticed a few things, usual behavior or?
 

Sometimes when I go over a bump, the car makes this shuddering noise that sounds like it's coming from around the transmission/drivetrain. Doesn't happen all the time, but it's definitely noticeable when it happens.

Also, sometimes going into certain gears (it's happened mostly going into 5th), it sounds like there's rubbing as I'm letting the clutch out. I can feel it in the pedal too. I'm at 29k miles and under both powertrain and bumper to bumper, so I can take it in. Just want to know if anyone's had similar issues before i surrender her to the dealership

Hows the clutch?

Sometimes it's smooth as butter. Other times it's chatty and rough. Also very difficult to get into gear when it's cold. Guess we'll find out, got an appointment on monday.

I know that exact rattle / thump , thud you speak off as well, my ZL1 has the same thing, I think all or most 2012-13 ZL1's were affected by it, some say make sure all suspension parts are tightened down , no loose bolts , nuts etc, another said change out the fluids. So idk i am going to do the fluids and if still there take it to the dealership.

Here are few links that talk about this thud.
http://www.camaro5.com/forums/showthread.php?t=520661

http://www.camaro5.com/forums/showthread.php?t=520177

If you or your dealership solve this, please PM me i need this info as well!

I'll be having them change the diff fluid out for sure, it's been groaning when turning at cold Temps since I got her

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Any Updates or Luck?

They flushed my clutch and differential, seems better so far. I still heard the thudding but it didn't seem as bad. They said they looked over the whole front end and didn't find anything. It sounds like a very "thin" thudding, almost like the bottom skid plate is rattling against something.

I noticed a rattle on my car while I first started driving it. I decided to put the car up on my race ramps and take a look. The lines that run from the trans back to the diff seemed like they had a lot of movement and would bounce off the heat shield under the car. I decided to place a heavy duty zip tie to limit some of the movement, and the sound went away. Just a thought, might not be the same sound you are hearing...

Chatty and rough is uneven wear on the flywheel, could come from over slipping the clutch. If its minor then normal use and down shifting will clean some of it off the flywheel. If it's excessive from major slipping then the flywheel is burned and its not going away. Bleeding the clutch will help, its too late now but you should have examined your brake fluid before they changed it to see what color it was or if it had any slag floating in the reservoir.

If you are feeling issues in the pedal when engaging the clutch at the same time you feel this thump its drive train. You mentioned that you hear rattling. If it goes away when you depressed the clutch could be the inner clutch. When they start to wear they will rattle with the drive line engaged in neutral or when driving.

The M6 is normally hard to engage when it's cold, but soften's up with in a mile or two. Some go to an aftermarket fluid that has better results, but I have been happy with the GM fluid and change it once year after the last season track event and winter storage.

My problem sounds more like the problem VRZL1 outlined above. doesn't sound very mechanical. The clutch issue I outlined seemed to have been remedied by the flush after about 50 miles of driving.

Interesting, i dont think its the lines or clutch , my clutch feels fine and break fluid seem normal, brakes are nice and tough, only 20k miles not 100k... So im with Spadz here, did your dealership check the suspension parts Spadz?

Changed my fluid 1's so far, plan on doing 3 flushes, the fluid inside was black with metal shaving goop type stuff around both caps, so 3 flushes and figure 8's should help settle this, i think dealer only fills yours up once if you don't specify. And i was quoted 220$ for 3 bottles, and about 400 in labor... bought 3 bottles on amazon for 40$ same exact ones. and did labor myself.

They checked the whole front end and didn't find anything. They also followed the TSB on the differential

I had two things that where giving me a rattle. Check the exhaust for rattling against the cross member plate the goes across the bottom of the tranny tunnel? When I went to a 3in exhaust mine would rattle from time to time, I placed some thick washer under it and the rattle went away. Other was a loose front sway bar bolt.