What you've experienced is really not that uncommon at all. Full siblings will also usually differ somewhat in DNA composition since each sibling may inherit differing amounts of a certain ethnicity from each of the parents (think of how different siblings with the same parents can look for instance). Besides, since only a great-great grandparent was allegedly full-blooded Native American, assuming she was full-blooded, that's still only 6.25%, so 2% is not too far off.

As for your Jewish/Middle Eastern ancestry, that may have simply been lost on you. That doesn't seem that you don't have that ethnicity as a part of you, but that you simply didn't inherit any DNA or genetic markers that signify that ethnicity, unlike other family members who did. It sounds odd and counterintuitive but this is all a very new science. Try watching some of the explanatory videos offered on your DNA Home Page in order to gain a better understanding as to how the science and calculations work. It's really pretty neat.