Pathfinder assumes a min/max mentality in characters. It is an extremely codified system that rewards deep understanding and punishes seat-of-pants play. That is to say that you really should be using close to optimal builds of core character classes and a good party build with synergies. For example the Challenge Rating assumes that you have a good party, one that might contain good versions of a fighter, cleric, mage, and thief. If you have poor builds of those keystone classes, or even poor playing of those characters, you can run into trouble.
I'm assuming that your problem centers around just combat. Have you looked at presenting the group with a social challenge and see how they fare? Might give you some more data points.
Does your custom method consistently make lower CR encounters for your group than the by the book method? If so than I would look at your group and how they play. They may not be using the symmetries inherent in the system, as is.
You might want to look at your group's tactics and their builds. Rather than just let the dice fall where they may, make sure you are helping the group see the synergies between characters and their actions. For example, make sure the cleric casts their buffs on the right weapons and characters before combat.
How do their resources look after a typical combat? The CR methodology assumes that a certain amount of resources should be used during a typical encounter, where does your party stack up?
If what I suspect is true (namely that the group might not be comprised 'properly'), you can probably go back to using the CR method from the book and drop all this home-brew stuff, you will just have to do some hand-holding to get the group there.
Oh, and don't forget that half the fun of a combat can be in figuring out weaknesses before the combat, a la investigation! Sometimes players have their characters go head first without any knowledge of what they are facing...that can lead to disaster no matter what.
I wouldn't give up on the system as is; it works, very well I might add. The first few levels can be tricky for anyone, and can swing wildly in favor of either side of the combat. I'd stick with it and adjust things as you need; its okay to fudge a die roll here and there and allow your players to change their characters and feats and skills allotment over the course of the first couple of levels.
Also, are you playing the baddies the way they should be played? Or the way you want to play them, if there's a difference? Make sure you are playing them according to their write-ups, not according to your meta-uber DM brain tactics!