This is a brand new thing that's started happening since I installed X3e on a new computer. Very frequently, keyboard shortcuts will stop working entirely. This includes the default keystrokes, even the Space bar. It can last for 30 seconds or a few minutes, and then all of a sudden they'll start working again. Rebooting the machine doesn't make any difference. Has anyone experienced this before? Concurrent with this problem is that my PLAY orchestra sounds do not work (see other thread)

I'm having the same problem :(

I can think of a couple of things:
 
1. Make sure the Sonar window you are working in actually has the focus (click in it). For example, if the PRV is not the active window, it will not receive keystrokes form Windows. Clicking somewhere in the PRV ensures it has the focus. 
2. Since Play is also not responding at the same time, it may be that another process is interfering. Common suspects are: Antivirus, Windows indexing service, Dropbox or Onedrive (if any files used by the project are located there) or even a Wifi card. You can check in Task Manager / Details tab to see what else is running. Also check the disk tab and see what disk activity is going on while Sonar is unresponsive.
 
I always disable AV and Windows Indexing for the sample and project folders. 
 
Hope you both get it resolved!
 
 

I'm having the same problem.
 
Very frequently, not also shortcut but also all keyboard key working stop on only SONAR. (ctrl key is working when drag copy)
 
It's working okay on other windows apps
 
this problem appear often when open Rob Papen SubBoomBass Synth.
 
LOL