This, but it seems random when it happens, I can't reproduce it, only consistent thing is its at low speed.

Did they tell you anything about the noise?

Hey guys I don't know if this has been mentioned yet, it might be a breakthrough, but I had the idle dip with fluttering sound when slowing down. I have 2000 miles on my BRZ and it never went away. However, I just installed an axle back exhaust and it never does it anymore when it used to do it every time I drove. Maybe it's a back pressure issue causing it to dip. It will probably work with any axle back but I'm using a Nameless part.

They claimed that it's too new of a car for them to diagnos properly. They contacted Toyota and they are aware of it. Nothing can be done at this time until Toyota adresses the issue and a corrective solution for dealers. It's safe to drive in the meantime

Having the same problem with this noise, car is in for service, will post updates as soon as more information is discovered.

I updated the original post with a better description.
Is there a way to update the thread title?

So I've posted in reply to the OP and on two other topics similar in nature. I have the FR-S 6MT in Ultramarine as of last Thursday (yay!). After 300 miles, I can't begin to describe how nearly identical the sounds made by my FR-S clutch and transmission and diff sound to the 2006 6MT IS250 I drove from new until 2008 with 35k miles. The throw is a bit shorter which I like. But the clutch engagement feel, downshift "jar of marbles" sound under 2500 RPM when coasting/slowing down, and the mild "thunk" of the rear diff when engaging first gear from neutral are so uncannily similar, it is (in my mind at least) the same issues that bothered some early MT IS250 owners while some weren't bothered by it. I haven't looked at clublexus.com in years, but there were a number of long threads about IS250 MT drivers going back and forth about whether the sounds were good, bad, doing damage, or normal for this gearbox. The IS250 is about 3400 to 3500 lbs with an engine of similar power to the FR-S. I drove the hell out of that IS and never had issues with the transmission or clutch or diff. for 35k miles. The noises never got louder or worse - just there. If the clutch and tranny could handle a car weighing 700 lbs more than ours, I don't think long term durability will be an issue at all. I understand why many are concerned, it's a brand new car after all. But I feel totally confident in my FR-S drivetrain knowing how tough it was in the much heavier IS platform. I would certainly make note of these sounds with your dealer so they document your input. If there's a "fix" or enhancement down the road, having any such issues documented should make your case. That said, I'm gonna drive my FR-S just like my IS, but with much more fun to e had!

I'm getting what sounds like someone poured a jar of marbles in my gearbox when decelerating in 4th gear.

I took mine to the dealer and they said the same thing. Toyota needs to understand that since most of us have this issue it doesn't make it "normal" but even worse. Like if everyone in the US gets sick, that doesn't mean its "normal."

I've noticed this rattle since day 1. Only happens when the engine is in operating temperature. When it's cold, it doesn't rattle. It sounds like some metal shield that's loose.

Even if it's normal, I want to know if there's any way to muffle the noise since it's really annoying my OCD ass.

hmm are there any updates regarding this? i just purchased my frs 2 weeks ago and i'm starting to notice this sound as well. it happens when just throwing the gear into neutral and braking as well...

I have the same issue. I thought it was due to my Injen intake, guess not.

I just noticed this sound as well... But I was in neutral and pressing on the brake getting ready for a 90degree turn... Not sure where it came from I've only heard it twice so far

Not sure if this is the same sound but I noticed a sound like something is spinning loosely when I am braking to a stop in neutral. Anyone else hear anything like this?