Rad, I am re-adding the message about the casting level for spells. I need a little more information about the builds that give unexpected caster levels.
What is the order of classes for the builds you listed?
e.g. cleric, then druid, then shifter OR
druid, then shifter, then cleric OR
druid, then cleric, then shifter?
To add bonus casting levels from say PM levels, you have to determine whether the spell being cast is arcane or divine.
If it is arcane, then you have to decide if the caster has 2 arcane casting classes (consider wizard/bard/PM or sorc/bard/PM or wizard/sorc/PM). Or, if divine, if they have both druid and cleric levels.
And decide which of the classes is casting the spell (so that all your 28wizard spells cast at the proper level instead of at level 2bard for a 28wiz/2bard/10PM)
Though I haven't worked on it enough to figure it out, I think shifters screw this all up. As a Rakshasa, you cast acid breath, but potentially have no arcane casting levels. Or a drider casting magic missile or a spectre casting negative energy burst.
The scriptset I used to implement this was designed to add bonus levels for PMs (and incidentally RDDs fit in nicely too). So the function that checks to see if you have arcane levels only checks your first class to see if it is arcane, if it isn't, then it assumes your second class is arcane, since otherwise, there'd be no possible way to have taken PM levels. So I'll have to think about how to have it account for shifter properly. It likely isn't hard, but I haven't had very many good days where I can focus on any of the ideas I've been working on long enough to make progress. Until then, enjoy whatever benefits it has