Every time you click "Run" in Appcelator Studio to the iOS simulator, the IDE will beachball while rebuilding the workspace once the built app is launched in the simulator. The IDE can block for 5-60 seconds depending on the machine. While beachballing, the IDE cannot be used. Nor can you view anything being logged by the app.
(Studio always beachballs for 1 minute for me.)
The CLI is changing the following Titanium SDK file whenever you do an appc run to the iOS Simulator.
Appcelerator Studio monitors for any Titanium SDK changes under the below directory. If at least 1 file is added/changed/deleted under this directory, then the IDE will "Rebuild the Workspace". The above file change is triggering this behavior for iOS simulator builds.
You can monitor file tree changes with the below node.js script. You'll need to change the below path to your equivalent SDK version folder that you plan on building with (don't forget to change <UserName in path) and then run it in the terminal via the node command line tool.