I have 2 bikes one with chain stay brake mounts and one with seat stay brake mounts.......Fly brakes spec sets specific for both mounts.........

Are they really that different? Can on set be interchangeable?

Traditionally people have run the same brake in either position. However, when brakes are upside down on the seat stays, the cable pull is not as straight as it could be. You're basically pulling the brake in a direction angled slightly off directly horizontal, which U-brakes were designed for.

So if I remember correctly, FLY had some modification in the brake arms that was intended to create a straighter pull for seat stay brakes.... I may be wrong, this is just what came to mind.......

Chainstay brakes with the cable running through a hole in the seat tube (the old school way) actually work the best, for the simple reason that the cable pull is dead straight and there's a short straddle cable which is less flexy.

FLY actually had a good invention on the Mosca--chainstay brakes with ultra low mounts so you could still run small sprockets.... but it didn't catch on.

Exactly. The Fly brake arms have an angle to them to create a straighter brake line. The CS version will have more of an angle & the SS, less.
I'm sure you could use either brake just fine & still get good braking though.
-Bill

Maybe its a product of growing up working endlessly trying to get calipers/pitbulls/etc. and a rotor/spinmaster/gyro to work on polished rims or, even mags, but I've never understood when some of the new school kids talk about how chainstay brakes don't work as well. I can set up mine to work like disk brakes in a car. Once chrome rims and 990's came out I never had a problem stopping, and I happily put away the Simple Green/soda/etc. on the rims to get them to work.

They still do it on the Pantera also and yes it works great. I own one and love it! You were right regarding their brakes also, the 2 different versons have differnt angles ont he arms to make up for the different angles that seatstay vs chainstays are at.

I agree with D. I can get any pair of 990 style brakes to work very well. I'm sure it's from working on mag wheel/rotor/crap for so many years...

I never noticed a difference between chainstay vs. seat stay location.