My suspicions are more focused on his citizenship status in college, when he had the ability to renounce his Indonesian status. Since birth certificates apparently carry notes about such things, he would have good reason to keep it hidden, particularly if he used foreign status to get financial aid.
I agree that is where he wrote from after they returned back to Hawaii. If they were all in Kenya, it was after 2 years Obama Sr. was in college in Hawaii who likely took a summer break in his home country with his pregnant wife before starting the next semester in the fall.