I was a total idiot and didn't clean my brand new Shilen stainless match barrel after shooting it for the first time. After 6 months in the safe I take it out to clean today and I notice this in the rifling. The hopes soaked patches did not come out blue or with visible signs of rust. Please tell me this is copper fouling and not rust.

 

Looks like copper fouling to me. While stainless will rust it has to be an awful cheap grade of stainless to rust after one range trip.

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^yup, has to be cheapo high carbon stainless. Probably copper fouling. Worst case, shoot it a few times and be sure to thoroughly clean it and oil it after.

I doubt it's cheap SS, I don't think shilen would use cheap SS in their select match barrels, but you never know. It is ferritic though, but so are my stainless revolvers. Anyway, I will pick up some copper remover and see what happens.

I'm not much of a metalurgist, but I understand that unless its 'passivated' (an acid bath to remove anything that can corrode on the surface), stainless is resistant, but not immune to rust.  Minute particles of the tooling used to machine the stainless - usually carbon steel - also embed themselves in the stainless and can/will rust without passivation.

I've had autoclaves and other stainless steel items passivated in the pharmaceutical industry but I've never had a SS barrel passivated.

From your pics those are copper deposits.  You can use a chemical copper remover or a non-embedding bore cleaner like J-B Bore Cleaner.

Eventually the bore will smooth out and you'll have reduced deposits.