It started when the game crashed. I don't know why, but when I reloaded the game (I had just jumped to a new beacon, so it managed to save) the bug started.
Basically, the backgroundwas replaced by flickering orange and white. One or two frames of the proper animation survived, but it made the game almost unplayable. The flashing paused if I pressed space to pause.
The hacking system also stopped working entirely. It didn't even launch the probe, though it did sometimes consume a drone part anyway.
It didn't go away when I jumped several times to different backgrounds, even when I went to the next sector, or when I quit and reloaded the game.
If the screenshots don't show up, they're also here:
http://steamcommunity.com/profiles/76561198072440388/screenshots/?appid=212680&sort=newestfirst&browsefilter=myfiles&view=imagewall
These screenshots aren't from the first beacon, they are from a later one in the same sector.
The original beacon (where the game crashed) was in a nebula sector, no other special environmental dangers, unvisited, not the exit beacon, well ahead of the fleet.
The beacon spawned intruders into my ship, I paused, opened the airlocks, tried to make some crew check the rooms to see where the intruders were, then pressed enter because I realised I could see which doors they were trying to break down and then the game crashed.
I still have the save file which still shows this broken background, and could send it to an email address if necessary. This hasn't been mentioned anywhere else, so I assume it is very difficult to replicate.