The only issue it had was when it first arrived, it worked for about 15 minutes and then just died. Completely dead, wouldn't do anything. I thought it was the power supply, called Lionel and they sent me a new one. Then it was fine, worked perfectly for 6-7 months, until the upgrade problem.
Then when I had the upgrade problem it died again with the new power supply, same as it did before. After fiddling with it for a half hour or so, I finally got it going again (but it still would not upgrade). Seemed like a loose connection where the power supply plugged in, but I really was never sure what it was?
I explained all this along with the upgrade problem to Lionel when I sent it in. When I got it back I tried the original power supply I thought was bad and it worked. Not sure what the problem was the first time either. Maybe overheating power supply? Haven't tried the old one long enough to check that theory, only tried it briefly.
I never had to reboot it or had signal problems or anything like that after getting the new power supply. As I said, it worked perfectly with absolutely no problems (at least that I could see) until the upgrade attempt.
Mine Legacy 990 is one from the problem batch that was delayed for almost a year when they had the part problem and they had to send them back or rework them or whatever was wrong that caused the long delay in releasing them. I finally got it about September 2014 after ordering it in Sept 2013. It was almost one year to the day from when I ordered it and was originally supposed to be delivered in like Nov 2013.
The good news is that it has also been working perfectly since I got it back from Lionel after the upgrade fix. I have upgraded once since it came back and it upgraded without a hitch, worked great. Which now reminds me the first upgrade was 1.52 to 1.53 and the one after I got it back was 1.43 to 1.54.
Sorry to be so windy here, but though the whole ordeal might possibly shed some light on your problems. I would still explain, in detail, all the problems you have had as best as you can to Lionel. They ask for all that on the RA form as I recall.
Good Luck