Vidman,
Pathfinder is, to me, meant to facilitate story telling. Your group and you are telling the story of some adventurers (their part) vs the big bad world. The part of the GM is not to 'be' the big bad world, only to describe it and adjudicate what happens when the party members interact with the world.
The GM - referee really - gets to decide what happens when the adventurers interact with the world. If they party is completely lopsided in power, as in 1 guy doesn't play well with the others, you need to do one of several things (not all described here) but in limited form: reduce their power, scale up the rest of the group, remove the player, and/or push down how well they do in their checks. Again these are not all of your options, and I'm not telling you what to do.
If the whole party is over powered vs the monsters, scale up the encounters. Add terrain features that make his default checks harder. Add environmental factors that make the same checks harder. Give the monsters similar mythic abilities that he has. Give the monsters the same advantages that the PCs have. Add PC levels to the monsters, sunder gear, target potions or scrolls, damage armor. Or other such possibilities.
You, the GM, are the game referee. If the playing teams - the players and the world - are not balanced at all, then you may as well just come to the game with pre-printed 'YOU WIN' stickers and hand them out and then go on to the next thing.
Pathfinder, and other RP systems, (Again -TO- -me-) are about telling a story. If the story is going to be 'You guys won through no challenge at all", people are going to have less enjoyment then they could have had.
In every case, Talk to your players, individually and as a group, about the auto-winning, and that you are going to take steps to present more of a challenge for them. Really, -For Them-, not for you.
TL;DR You can fix it, if you and the players want to fix it, and you are going to have to have them help or it isn't going to get better. -imho
Em Zee