Have you ever read about Metabolic Bone Disease (MBD)? Squirrels require a fair amount of calcium in their diets combined with a relatively low amount of phosphorus and standard foods are just the opposite. The first thing I would try doing I getting some calcium into him and see if there is any change in his behavior. The easiest way is to buy a bottle of fruit flavored Tums - the indigestion stuff is all calcium and is flavored.
https://thesquirrelboard.com/forums/...dated-3-31-09)
Please bear in mind this is written for a 1 to 1.5 pound squirrel - I would cut all of the numbers for recommended amounts at least in half or 1/3 for a chipmunk.
Get the Tums. You can see if he will just nibble on a tablet, but if not you can mash it up and mix with water or even hide it in a tiny blob of peanut butter. If you begin to see improvement over the next couple days you know what the problem is and we can help work with you on diet so it doesn't happen again.