Does anyone know how Magic Vestment works? If you have a Shield +1, and as a 9th level Cleric, casting Magic Vestment upon the shield, does the shield become a +3 or a +4 for the duration of the spell?
Magic vestment provides an enhancement bonus and the +1 bonus from the shield is also an enhancement bonus. Bonuses of the same type do not stack (with a few exceptions, like dodge). In your example, the shield would become a +3 shield, ignoring the shield's normal bonus of +1.
That progression would imply that +5 is reached at 13th level (if I'm reading you right), which contradicts the spell's description of "maximum +5 at 15th level".
The language "+1 per three caster levels" is quite clear. The other progression is denoted by the words "for every X levels of experience past 1st, you gain an additional Y", as given for magic missile.