This is still an issue. I use a lot of USB KVM switch to hop between two computers and it takes about 3 minutes of freeze time for the simulator to catch on. You can see the cursor move around the screen, but none of the simulator controls (whether during flight or in the menu) are active until the three minutes passes. If you are insistent on clicking around, the sim will CTD.
They have been struggling with this since alpha/beta and actually got it right somewhere around SU2/SU3, but it’s broken again.