So, I've reached the water temple and am fighting the Juggernaut but I can't seem to hurt it at all. But by most accounts, the juggernaut isn't that tricky.
I'm looking at the damage info, Its telling me it has DR 20/Magic. But my fighters both have magic weapons and even my magic missiles are doing nothing.
There's a value stated as "Invulnerable" that seems to be soaking up the damage but I have no idea what this indicates.
Anyone know what I'm missing here?

Need a magic weapon that does slashing or bludgeoning[Not sure on what kind of damage you need, been a while since i last play the game.So maybe wrong on needing slashing or bludgeoning. If a magic slashing or bludgeoning magic weapon fails try piercing.] damage in order to break dr for the juggernaut.
The juggernaut has 20 spell resistance,which is why your magic missiles are failing. Your caster failed to get pass the monster's spell resistance.

That is all i can say with out knowing more about your party.

Well, Its DR 20/Magic, like I said, so it doesn't matter the damage type. And just to set your mind at ease, one guy has Bludgeon, the other has slashing.
Its not the SR. The magic missiles aren't failing. They are doing no damage when they do get past the SR.
I reckon I just hit a programming error as when I exited and came back I was able to hurt it fine (It still owned me, but at least I could hurt it)
The "Invulnerable" value on its damage stats wasn't there this time.
I had the same problem with one of the werewolves but a reload sorted that one out as well. (before you say anything, There are two werewolves. I could hurt one, but not the other)

So yeah, no idea what happened or why but a reload fixed it...

A few suggestions:

Do any of your melee "warrior" types (fighter, barbarian, ect) have the power attack feat? If so, switch that on to a reasonable damage boosting number. In order to help offset the attack bonus loss of using power attack (and just to make life easier for any challenging battle), I'd suggest buffing up your warrior(s) with spells like bless, prayer, aid, bulls strength, and greater magic weapon.

You can also throw some enchantments on your warrior weapons with craft magic arms and armor. Belts of strength made via craft wondrous items can also be very helpful and eliminate the need for buffing with bulls strength all the time.

Didn't experience the bug you mentioned personally, but the above advice should be helpful in overcoming high damage reduction in any situation you encounter it.