I have the same issue. To clarify for other posters with other scanning issues, this particular flavor:
- Allows hacking to work as normal
- Allows tab scanning as normal for gameplay purposes (highlighting objects)
- Allows the standard 'Info' tab to be accessed while scanning
- Does not allow any mission or story based additional info to populate and does not progress missions where scanning is a requisite step. These opportunities are always characterized by a gold/amber color when scanning and a magnifying glass, but when experiencing this bug, this magnifying glass icon always has an additional stopwatch icon overlaying it in the bottom right section
From a story perspective, this means that the blood trails and dead bodies normally providing additional flavor text on missions don't work. It means that some story decisions also automatically fail (you can't scan a ripperdoc patient when asked to, for example- it just doesn't register).
Most significantly, it means that certain missions are irrevocably broken. You just can't work around Ghost Towns or Gimme Danger's need to scan for the quests to proceed.
I have had Johnny pop up to have conversations with me as part of a handful of side gigs (such as the one where I took the non-lethal route to save a monk). Unlike what some others suggested, this did not clear the bug. Nothing has.
I'm not certain which mission triggered it for me, but I've 30+ hours past the last save where it wasn't in effect (all spent clearing icons on the map, since I can generally do that, although it means I fail some side objectives or are locked into some choices). I know it was working in Disasterpiece.
I also had the issue with the car not spawning for the peace offering gig. Not sure if that's related or not.
But once I exhaust all of the remaining map icons, I'm fully dead in the water. I'm not replaying 30+ hours of assaults and side gigs, not now in the current state.