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Everything you ever wanted to know about ability scores:
Pathfinder SRD: Ability Scores
To summarize:
Temporary bonuses, ability penalties, and ability damage do not count as changes to ability scores. They have defined effects (listed in the above link) and do nothing else (unless otherwise noted).
Only "permanent" bonuses (after being in effect for 24 hours) and ability drain cause your ability scores to actually change.