It's the same with the debug command on the test servers being in this order. I haven't had issues yet with GTL since my current setup can't run PokeMMO, but I can imagine the frustration since HP/Atk/Def/Sp. Atk/Sp. Def/Speed is what I know
I believe it has no change to your encounter/shiny rates. The only thing getting a capcha will affect is your number of encounters since you have to stop running back and forth to do it.
Kek won
http://replay.pokemonshowdown.com/vgc2016-317508317
http://replay.pokemonshowdown.com/vgc2016-317511039
http://replay.pokemonshowdown.com/vgc2016-317514442
Blue won
http://replay.pokemonshowdown.com/vgc2016-314542303
http://replay.pokemonshowdown.com/vgc2016-314545312
http://replay.pokemonshowdown.com/vgc2016-314547427
Fighting Blue right now http://play.pokemonshowdown.com/battle-vgc2016-314542303
Round 2 http://play.pokemonshowdown.com/battle-vgc2016-314545312
Round 3 http://play.pokemonshowdown.com/battle-vgc2016-314547427