I had the same problem with my base almost 2 years ago, as I said above. Had to go back to Lionel for repair (it's been just fine since). This seems to be an on going problem that seems to pop up occasionally. I have the cable that Mike Reagan recommended in the video. It's the only cable I have ever used for this so it wasn't the cable in my case and the remote has always upgraded without a problem. It's a problem with the base.
Received back today from Lionel. Return letter states that the communications PCB was replaced in the base unit.
I got mine on the latest software on the first try for both. 
I had to do it twice on the base and a couple weeks later I had to send the base in for weak wifi communications. Not sure if there was a connection. That's the third time in for that 990 combo.
I have 3 sets for overlap of units broken and in for repair. How's the 1 L system doing?
That's good news, and thanks for reporting back about what was repaired. Good information.
Received back from Lionel. Return letter states that the communications PCB was replaced in the base unit.
Now it works like a Swiss watch!! Thanks Lionel service for the super-fast turn around!!
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