I cast Color Spray with my illusionist gnome.

the Will Save DC should be 10+spell level (1)+intelligence modifier (4) + spell focus: Illusion(2) = will save needed for mind spells: 17.

However when I cast this from a scroll I made on troglodytes (and other creatures too) it says the save is only 14.

Why doesn't this work right? and can it be fixed? Or does it have to be cast as a spell not a scroll for it to have the total DC of 17?

I think the DC for all scribed scrolls is a certain, pre-determined, number. I could be wrong though.

You casted from a scroll, it's the same with wands and not a bug.

If it is from a scroll, it will not take into account -your- intellegence score or -you- spell focus, it relies more on the person who crafted it in the first place.

I'm almost positive not in EfU, for instance, all scrolls of magic missile will be by a level 3 caster even if the crafter is level 40

This is the case, I believe. On another server a sorcerer of mine crafter a scroll of Greater Magic Weapon. It should have been +4 Enchantment bonus, however, due to the nature of Scribe Scroll it was only a +3 Enchantment bonus no matter what the level of the scribing mage.

There is no bug here. Scrolls, wands, and devices have a set DC that is not modified in any way by the caster.