My bad -- I thought you were proposing a possible explanation as to why it
wasn't working.
Which would have definitely explained the "why", if the OP had been using Calibre Companion and opening books from within it. But since the OP never said anything about using Calibre Companion, there must be some other reason why
it doesn't work.
I have no idea whether adding the books using CC and opening directly from Books would work -- probably, since it is apparently the browser download that screws things up, and CC acts like sideloading?

But I still want to know what it's doing differently when downloading from the browser...