RNG is CG's employee of the decade. They also give the AI advantage as compared to players in a few circumstances, and have admitted so in the past. They have certain ships and characters that get higher priority as targets over others, and so on. If your capital ship is the exact same as the other, the coin flips and you will notice runs of going second often. (Just confirm that your capital ship leader is R9 and has all 6E mods on?)
As far as the punishing one, the AI's is stealing your stealth most likely because yours is stronger. It's a weak zombie in ships, though there might be other issues with it too that aren't working right. CG's priority for bugs they create in PVP situations is fairly low. If it was beneficial to players in PVE, they'd be sure to fix it fairly promptly.
Try an alternate counter? Check out bitdynasty's youtube channel or his webpage. He has counters for lots of things, including fleets. You might just want to use other options to get through..
