It seems while the US knew about this it had a spy within Kaspersky and was their source for finding out what they were up to. The accused spy was arrested by the FSB recently so likely the US no longer is willing to take on the risk of allowing Kaspersky to run on us govt machines. Marco Rubio appeared to hint at some classified info about known govt risks of dealing with Kaspersky. Additionally the second link mentions Kaspersky is moving into protecting critical infrastructure, which seems notable giving the sudden frequency of mentions of the weakness of US infrastructure to network attack.
The problem with classified security stuff is you never find out the full story. Only bits and pieces around the edges of it. It's almost never in their best interest to reveal the depths of what they know because it exposes their methods and awareness.
https://www.cbsnews.com/news/russia-treason-fsb-spies-kasper...
Earlier article on then working with the FSB.
https://www.bloomberg.com/news/articles/2017-07-11/kaspersky...