Check the seat post, basebar and stem bolts, and quick releases.

I've often found the creaking noise on my sc is NOT coming from where it sounds like it's coming from.

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Agree with Steve. Whenever I had creaking in my SC I always thought it came from the BB/drivetrain area but it inevitably always came from the cockpit area.

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Check stem, seat rails, seat post, QR. Remove, clean, apply light grease, reattach, and 9 times out of 10 the noise will go away.

You can play the isolate the creaks game. If it's happening out of the saddle then it isn't the saddle. If it's happening when not holding onto handlebars (do this on a trainer HAHA!) it's not the stem. Etc....

Possibly a cracked bottom bracket area. Happened to me.

check the chain ring bolts. have your mechanic do it. greasing those suckers can fix a creak sometimes.

are you 100% sure it is not coming from the front end?

Never once seen chainring bolts cause a creak.
The most usual things are rear wheel creaking in frame.
Undo skewer, rotate axle and reseat wheel, do skewer up.
Creaking bb.
If the mechanic has had it all apart, unlikely.
Headset components creaking in frame.
Pull apart replace any dead and refit with plenty of grease.
Handle bars and stem.
Same deal, pull apart grease all bolt heads and threads, refit bars and stem with carbon paste.

Some unusual things that may appear.
Cable casings creaking in frame where they enter. Squirt of grease will fix.
Water bottle cages creaking. Grease bolts.
Check the chainrings, if they are worn the chain/ chainring interface can creak.
Likely as you are also dropping chains.

Thank you all for your input. Im taking the bike back to the mechanic to go over everything, especially the frond end. Hopefully that takes care of it.

OP mentioned bike is new with 500 miles and that creaking started after chain suck incident. So prolly nothing wrong with ring wear. This chain suck is common on SC. I'm not sure I've ever heard of a common reason. Maybe chain length contributes. But wrapping up and jamming between the BB and chainstay happens all the time. Lots of these frames around with the protector and paint sheared off back there. I haven't seen one damage the BB90 frame area because it is all internal, but I suppose with enough force it may be possible to crack the frame at the bearing seat.

OTOH the early SC's had an issue with the centering nut on the top headset bearing that the stem clamps onto. This shouldn't be an issue this far into the series, but the end result was a lot of creaking. The top bearing is tiny so tolerances are important. Checking that installation is a good idea. There were also some recent photos on ST of one of these front ends put together totally wrong from the shop, so it can happen.

The strange thing is the mechanic went through the bike already and sent it back creaking. Hopefully it is headset adjustment or something even simpler like the rear wheel skewer you mentioned.

I just removed the rear skewer and re installed it, the loud creaking noise is now gone. I now only notice a light creaking noise when I am out of the saddle and aggressively putting power down, sounds like its from the base bar or the small diameter bar the the arm pads mount to. Those of you that mentioned greasing the bolts and front end components, do you simply apply the grease between the mounting surfaces of the components? on the bolts?

Thanks again for all of your guys responses! Very helpful

Bolt threads.

And throw a $20 chain catcher on. Because, well, why not. Great and tiny investment to protect your frame for those rare times when the chain falls off.

Good luck. Hope it's nothing serious.

Threads cleaned and lightly greased. And use a torque wrench. A little grease on skewers is always a good idea too.

As I recently found, the SC front end is easy to assemble incorrectly. One thing to make sure is that all parts are clean when put back together.

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What wheels are you running? I ran into a similar situation this past weekend. I had just swapped wheels, when I started getting a loud creaking anytime I put much effort into pedaling. I had just installed new chainrings the week prior, so I thought it might be a crank/BB issue. Troubleshooting noises on the bike is a process of elimination. My first thought was that it might be the skewer. I threw different ones on, and still got the noise. I then put another set of wheels on, and the noise went away. OK, the culprit were the wheels (which only had about 500 miles on them). Guess what...turns out the one of the endcaps had loosened from the freehub. All I had to do was tighten them, and the noise went away!

Good luck!

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Im running Williams System 58 carbon clinchers. The free hub body was making some noise initially, my mechanic removed it and reapplied the recommended grease and the noise went away.

I don't have a SC, but I had a creaking on my Felt that went for weeks that I couldn't locate. Eventually found a thread where someone recommended greasing/oiling the spring on me Look pedals. Noise went away. Bike noises suck.

And under the head, especially if it has a taper seat.
If enough grease has been applied to the bolt thread, then it usually finds it's way to the bolt head anyways, but in some setups it is wise to put a dab of grease directly onto the bolt head/fitting interface.