Not sure if this was covered but there is also a potential issue with the main board in this unit not playing well with the Legacy system.
Some command gets interpreted as a full system shutdown as if the red halt button was engaged on the remote. It doesn't show up in all units nor is it easily repeatable. Lionel does make a replacement board that remedies this issue and it was an easy swap. MartyE has a really good photo outline of the process on his website.
It started with mine about a week or so after we added Legacy.
Does anyone have a part number for the replacement main board (or could post a link to MartyE's web site.)? My unit's main board has an issue that I would like to remedy and I have been told the main board was no longer available.