When I had this problem, I had it from the beginning so it probably wasn’t due to a specific component. However, it might work for you, too:
With the iOS Simulator in focus, select the menu item Hardware > Keyboard > Send Menu Keyboard Shortcuts to Device.
In addition, I use the Colemak keyboard layout and found that after making the selection above I also had to use the R as printed on my keyboard keys for the ⌘ + R command instead of the one I would use based on the Colemak layout.