I'm using the 1.11 Pokecube files, and I am wondering if the config that lets Groudon and Kyogre captures ignore their requirements is still around? If so, what am I looking for in the config files?

in 1.11 versions, there should be no capture requirements for anything besides mew.

the spawner blocks for kyogre and groudon are also gone in 1.11 however,

Well they keep breaking out.

does it say they "refused to enter the cube"?

They "broke out" of a Master Cube. Zekrom too.

Note the words "Master Cube" and "broke out". You shouldn't be able to break out of those in the Pokemon series. Why do they here?

that was a bug fixed in the latest version. they had capture rate of 0, even mastercube cannot catch something with capture rate of 0