It's not your fault you are doing everything right from what you've said, chipmunks are very much individuals. I've found all of mine to have very distinct personalities, just like the seven dwarfs, happy, grumpy, sleepy and so on. On top of that, chipmunks can be moody, they have off days, manic days and lazy days. So, no matter how many years you have kept chipmunks I don't think anyone would be able to say which two chipmunks are going to get on.
I do think it's worth you trying again, but this time let Alvin live on his own in the big aviary for up to a month. This will give him a good chance to establish himself and when you reintroduce Theo he maybe alright. Plus, in a months time we should be out of the breeding season, perhaps hormones are playing a part in Theo's behavior.
I found chipmunk behavior quite bewildering in the first years. One minute two chipmunks can be sharing some food together, the next one is chasing the other around aggressively. If at the end of the day they both end up in the same nest box, you can take that as a good sign that it's only squabbling. If Alvin spends most of the day hiding, and hardly venturing out of his nest then for his sake they may have to be kept separate. I don't think I can describe very well the difference between a pecking order squabble and a serious fight. But if you do witness a serious fight you will know it, it's horrible and quite shocking to see. In the meantime check on them both each day, look for nicks in the ears and bloody noses, as those are the places they often go for. Biting on the back and tail are also common, but this is often less visible because of their fur.
Stick with it, I've found after the first year or so things get much easier. As they get older they do calm down, and neutering can also help vastly cut down on the testorone levels in their bodies.