i havent had any issues(grinding gears, clutch slipping, etc...) ill mention it when i go for my first oil change unless something changes or gets worse. ive heard the noise in neutral, reverse and 1-2 shift. so i assume it does it all the time, but just cant be heard over the engine.

The transmission itself is Toyota's call and built by Aisin, I don't think it's a Subaru thing. As for the clutch, I am not sure.

I didn't know until I watched Lytheum's video.
I thought it was making noise on its own during idle without touching the clutch.
After I watched Lytheum's video, I tried pressing and releasing the clutch while at idle.
Mine makes the noise too and it's loud :o
I don't know if cars other than FR-S/BRZ makes this noise too, because I've never done this on any other cars.
I'm subscribing to this thread in case anyone find out any information about this noise.

The transmission is Aisin and it's a very close relative to the manual gearbox in the RWD 6MT used in the Lexus IS250. I drove a 2006 MT IS250 for two years, from brand new until 2008 (approx 35,000 miles). From my experience, I have heard VERY similar noises as described by the OP. I even had the infamous "jar of marbles" sound when shifting lower gears at slower speeds. I never had any mechanical problems with the IS MT clutch or tranny. I sold it to a work colleague and she and her husband drove it another 25k miles with no issues. I'm not saying you don't have an issue to be addressed, but I can say from my experiences the tranny and clutch did have a few quirky noises in my IS. BTW - I drove that IS hard and loved every minute of it.

That's the best description of the noise I've been talking about!
http://www.ft86club.com/forums/showthread.php?t=8344
I updated my post :)

i never heard it till the weather cooled off and i had the windows down pulling into my garage. with windows up i cant it.

Update,

Im still experiencing issues,

Shifting from any gear to any gear 90% of the time, unless its a super delayed long clutch in, and I mean like much longer than it should for any car, you can feel there is slack/play.
best I can describe it is that it feels like it takes a full second for all the force to be reapplied to the gears and actually start applying power to the drive train, its only when load is let of and reapplied, EG: starting from dead stop, shifting gear to gear 1-6. coasting in gear and accelerating.

Dealer has asked me to continue driving it until it gets worse. Its increasingly harder to have smooth shifts in the car now. I went and took another FRS for a drive, there was no WOT and only normal driving, was able to endlessly shift gear to gear, down shift, coast and accelerate with NO ISSUES @ all.

the clutch engagement sound however is existent even on there brand new FRS.

anyone else notice what im dealing with?

I will most likely be getting a new tranny soon, I understand its not easy for a tech to make a call of replacing a tranny so soon. But im taking it back mid august and they will make the call than.

Bu-Tang:
That sucks. Mine definitely doesn't do that. If you can feel that much of difference between yours and demo car, then something must be wrong. I hope you get yours fixed.

I just scrolled straight to the bottom to answer this. Sorry if it has been answered already.

It's the differential. It's normal.

The mounts and/or bushings are probably not the best. Personally I like the sound..... Because Racecar :)
I have several friends with 240's and other cars similar to this that all make the diff clunk noise.

Edit: I watched the video: obviously not the diff lol. But our car does still make that noise in the diff, for manuals.

I have the knock noise when pressing the clutch pedal. It doesnt do it when the car is off. Im thinking it may be related to the throwout bearing.

I have also been having difficulty engaging first or second if I come to a stop. I have to almost force it into gear.

Thanks for posting this.. I'll have to listen for this, and the delayed clutch engagement issue when I go test drive a BRZ/FR-S..

Hope you get the problem resolved.

My car makes this sound as well but there doesn't seem to be any performance issues.

I'll keep an eye on this thread.

Okay I watched the vid. That's messed up. I get the diff clunk when I engage first or second at low speed or from a stop.. which is normal.

u driving it all wrong!!!