The combination of short chain stays, a wide cassette on a 130mm axle, and a wide size difference between chain rings, like 50-34 or 53-39, will often cause the chain to rub on the inside of the big ring when using the small-small combination. This is quite normal. My Felt F5 did it. My Giant TCR did it. My Trek Madone does it. My 42 year-old Masi Gran Criterium doesn't do it, because it has a 7-speed cluster on a 126 mm axle and longer chain stays. It didn't happen with your steel rings because the teeth were probably a little bit narrower. When you fudged with the inter-ring spacing it stopped shifting properly because the derailleur is designed to work with a center-to-center chainring spacing that is proprietary to Shimano (and copied by FSA, SRAM, and others).

Small-small is your sacrificial gear combination. Just don't use it. For me it results in too much chain slap against the stay anyway, and with a 10-speed cluster I know there's a combination on the big ring that's close enough. I know some guys compensate by inserting a 1mm shim behind the drive side bearing or cup to shift the whole crank to the outside a bit. If you're really hung up on this you might give it a try, but it might result in too much cross-chaining the other way on big-big. And some guys say big-big is against their religion, so they don't mind.

And I apologize to the topic border patrol, but I thought I could just put this to bed. I promise not to do it again.