After GOG MP update my signal booster will no longer prompt for input data. Selecting Input Data simply returns to the opening menu. I have found, (by accident), if I attempt the input data selection twice then exit the booster and go to my Blueprint Analyzer , it will open with the frequency selection menu from the booster. It will use a nav data chit without asking me for the data source. So it appears the controls of the two devices have become crossed.
If you haven't already, use GoG Galaxy to verify your installation and repair any necessary files. I know, I know. Some people don't like to use GoG Galaxy, and I'm generally one of them. I was experiencing anomalous behavior (irony that) from my NMS installation that was only fixed by firing up GoG Galaxy and letting it do its thing. I've since turned it back off since I prefer not to use it at all.
I can assure you that I updated to the MP version, just in case there were other bug fixes or improvements besides formally enabling multi-player support. I prefer my NMS single player only, so I turned off the MP features. I do not experience the behavior that you report. I'm not saying what you describe isn't true ... far from it. It could be that when you applied the patch, or even a new installation over an old one, that something when wrong or got broken somewhere in the process.
Try fixing it with GoG Galaxy and see if the behavior goes away.