How to reproduce:
1. Create a new Unity project
2. Download the Input System package and restart the Editor
3. Create a new Input System Asset from Project Settings > Input (NEW) and check 'Run in Background'
4. Open Window > Input Debugger and double click on any device
5. Click on the Game View window to focus on it
6. See that inputs are registered when interacting with the device
7. Force a script recompilation by creating/reimporting a script
8. Focus on the Game View window and attempt to register some inputs

Expected result: inputs are registered immediately
Actual result: inputs are not registered until the focus is shifted away from the Game View

Reproducible with: 2018.3.10f1, 2019.1.0b6, 2019.2.0a7
Not reproducible with: 2019.1.0b7, 2019.1.0b8, 2019.2.0a8, 2019.2.0a9
Could not test with: 2017.4.23f1(New Input System not yet introduced)

Notes:
The issue does not seem to be dependant on Input System package version
Unchecking and rechecking 'Run in Background' in Project Settings > Input (NEW) fixes this issue until another script recompilation