Ojibwa is an Algonquian language spoken by Native Americans in the northern United States and southern Canada. Its pronunciation puts much less importance on differentiating voiced and voiceless consonants than English does, relying more on the expulsion of breath. A voiced consonant, such as "z," uses the vocal cords, and a voiceless consonant, such as "s," doesn't. This is one of the English language's fundamental means of differentiating words. In this light, "ajidamoo" could sound quite different to English ears, because it places less strict differentiation in the ways English speakers are used to. As a result, the "j" could have sounded more like a "ch" and the "d" more like a "t."
Furthermore, the Ottawa dialect of Ojibwa pronounces "ajidamoo" as "ajidamoonh," which would account for the "n" in "chipmunk."
As "ajidamoo" was further turned into a word comfortable for English speakers, it might have been influenced by the words "chip" and "mink." "Chip" would relate to the animal's small size, and "mink" would refer to the familiar animal of that name.
Chipmunks belong to the genus tamias, which is Greek for "one who stows things," named after the animal's practice of storing food for the winter. The commonly found Eastern chipmunk has the species name tamias striatus; "striatus" is Latin for "striped."