I don't think this is the problem, but lets check the simple things first. Where on the device are you putting the books? If you are putting them inside the .kobo directory, or any other directory that starts with a dot, they won't be processed.
Books not being processed usually mean that one of them is bad in some way. But, you usually get the black processing screen for a little bit and then it goes away without books actually being added. Or it hangs on that screen and nothing happens. If this is happening, then there is a book on the device that is preventing the processing. And it will keep doing that until it is removed. That basically means removing all the books that are not shown in the devices library and then adding them one at a time until you find the bad book. At that point you can look at it and try and fix that book.
It could also mean the database on the device is corrupt. If you are also seeing problems such as books disappearing or the reading status not being remembered, this is probably the case. Unless you have a known good backup, the simplest solution is to logout on the device. This will clear the database, restart the device and take you through the setup. Then it should load all the sideloaded books. If that doesn't work, you might need to do a factory reset.
The not restarting after a disconnect is something I occasionally see. I don't have a pattern for it (other than "happens at the worst time"). I usually wait a while and when I get impatient, do a pin-hole reset to restart the device.
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