The "yo-yo" effect is what happens when your fighter has bull strength cast on him one round and then is struck by a shadow. (score goes up, everything adjusts. Score then goes down, and everything adjusts again, making you recalculate everything.) Pretty much, its the ultimate in bonus-stacking bane.
I debated removing actual ability "increases" for similar effects. For example, Bull's Strength grants a +2 to hit, damage, and Str checks. Bears Endurance grants +2 fort, +2 con checks, and +2 hp/hd. While on paper, it seems like the same thing (net bonuses are the same) your con score isn't actually changing, so recalculating simply becomes a couple temp bonuses.
This would be coupled with the only effects that boost ability scores being stat-boost items (gauntlets of ogre power) and level-adjusted increases (every 4 levels). No more inherents, no more temp enhancments.
The final key would be to somehow re-work poison and ability damage, but I'm not sure how.
In the end, it seems an awful lot of work. While the net benefit would be a removal of ability score bouncing up and down, the work needed to fix it far exceeds what I'd want to put in to a game I'm playing for perhaps a year more...