For that, I could see two possible fixes.
1) All levels count together for XP, so a Combat 3/Magic 3 character counts as level 6.
2) Go with a flat-XP system - each level takes, say, 1300* xp. An encounter of equal CR gives you 100, +2 CR gives you 200, -2 CR gives you 50, and so forth.
*If...