This doesn't fit though, because computers, being devices can be programmed to run at certain times and not others.
I have first hand knowledge of this issue with a Dell L400. It doesn't start, gives no response with a "new" battery but will start without a CMOS battery or with the old CMOS battery. BUT my other Dell L400 doesn't start without a battery in it, but will start with a "dead" battery, but again, not the "new" battery I purchased as a replacement.
I don't think he fowled anything up, unless the original computer doesn't start with the original battery in it.
A "dead" battery isn't dead, just operating with a voltage lower than can be used, so there is still plenty of charge given to the computer to tell it the battery is there.
I think the suggestion is good to check everything, but it can be more idiosyncratic than just simple logic. Wish it were that simple.