Reproducible on 5.0, 5.1, 5.2;

Repro steps:
1. create a new project and import "Case691571.unitypackage";

2. Go to menu bar "Case 691571" -> "Build and Wait Test". This will start the script.

3. Wait until the script has built the player and prints into the console "Script is still running... Please focus another window than the Unity window (eg. open a browser) and then again focus Unity within 20 seconds.".

4. Switch to another application (e.g. the browser). The script continues to run in the background.

5. Switch back to Unity. The script will almost instantly be aborted (and it should not because it called "LockReloadAssemblies").

Repro project contains a script showing the issue. The script will build a player and then call "LockReloadAssemblies". Then it waits for 30 seconds. Finally it prints "Test finished." If you see "Test finished" everything is OK. If you're not seeing it, the script got aborted by the assembly reload (which it should not have been).

Workaround: don't switch focus from Unity editor;