When opening a character that was saved with multiple temp bonuses, only one was saved.
To recreate - using the Pathfinder RPG Core Supplements create a 2nd level fighter and give 2 or more temp bonuses, spell/condition/ability in any combination, and save. When the character is reopened only 1 temp bonus is applied to the character.
One other thing I noticed. If the temp bonus has more than one variable, like energy drain (penalty to hit points, saves, to hit & skills), only one variable for that temp bonus is saved in the character.