Hi Sheila, welcome to the chipmunk forum, and an interesting problem which I bet many others have experienced.
Yes it's quite normal when you have more than one chipmunk for them not to sleep in the same nest box. It's also common for them to suddenly up sticks and move nest boxes if they have a choice. I have a couple that seem to sleep in a different place each week, sometimes together and sometimes not. So it's a good idea to provide more nest boxes than you have chipmunks. Although quite often the spares will be used as larders.
From what you say I'm guessing these two are brothers, which means they should be used to each other. Also, as your able to go inside your aviary it's plenty big enough for two. If you can ever consider a chipmunk to behave normally or rather typically, I would say that Sprite is behaving typically. Most chipmunks are very lively, and once they have got used to you they should be quite inquisitive when you're with them. I've also had chipmunks that behave like Timmy, in a new home the shy ones just want to find a place to hide. You won't do any harm by investigating where you think they are nesting. Probably best to do this when they are awake in the daytime. Slowly as you can, put your hand in to each nest box. If you find Timmy he may make a soft growling noise when you touch him. He may even try to bite you, but if he's still young the bite should not break the skin. Investigating their nest boxes is something all owners find themselves doing. It won't upset the chipmunks much, they don't hold a grudge or move out just because you put your hand in. But it will put your mind at rest that Timmy's OK, and is useful to know where he sleeping. I don't recommend that it's something you need to do on a regular basis, but as you have only had these a week you will want to know they are both alright. I've found young chipmunks do not have the brilliant agility they gain when an adult. So it's conceivable that a young chipmunk in a new environment will take a tumble due to a misjudged leap, so you really want to watch both of them running. Looking out for any limping or bloody noses. But I must say the chances of a broken bone is still very rare, but I think I would want to check Timmy out if he was mine.
If you have the time and patience it might be worth spending some hours in their aviary or just outside so you can observe what's happening. But I have known a chipmunk to stay curled up in it's nest box for four hours or more, when it should be up and running around. Chipmunks quite often take a sleep during the day, often around 1pm, and I find their most active times are between 7am – 1pm & 3pm – 4-30pm. But this will vary on time of year and the chipmunks temperament, as I have ones that are up a 6am, and other s can stay in bed until 10am.
To sum up and I hope put your mind at rest, Timmy's behavior although not typical is not that uncommon, it is very early days for both of them in their new home.
