Adding a little bit more detail to my comments

A try-with block is defined as follows:

try(...) {
   ...
}

where the argument in parenthesis needs to be an instance of java.lang.AutoCloseable. An example is the class java.io.InputStream, which is also the class for System.in.

A try-with attempts to automatically close its provided resource, once the block is left. Depending on the used resource, it closes all its own child resources as well.

Taking your example, you have try(Scanner scanner = new Scanner(System.in)), which uses Scanner as resource. The scanner itself uses System.in as resource. Once the try block is left (when } is reached) it tries to close its resources, which is the Scanner instance. This instance also tries to close its resource, the System.in.

Once System.in is closed, you can't get any input from the console anymore (at least not with some additional work, I think...).

Concretely, in your second example:

while (!input.equals("q")) {
    try(Scanner scanner = new Scanner(System.in)){
            ...
    }  // <--- The block is left, scanner is closed, System.in is closed
} // <-- start a new iteration

Here after just one iteration, System.in gets closed. Sure, you create a new Scanner in the next iteration, but System.in remains closed, that's why you get your exception in this case.

Your third example:

try(Scanner scanner = new Scanner(System.in)){
    while (!input.equals("q")) {
        ...
    } // <-- start a new iteration, while still in the same try block
} // <-- only after the while, your resources are closed

Here you're looping your while, while still being inside try. So no resource gets closed, until you leave while and try. That means, the one Scanner remains intact and with it the one System.in. This allows you to keep reading from the console until you're done looping.

try-with-resources provides a guarantee that AutoCloseable resources, like Scanner, will always be closed. Closing is added implicitly by javac approx. as

Scanner inputFile = new Scanner(file);
try {
    while (inputFile.hasNext()) {
        ....
    }
} finally {
    inputFile.close();
}

BTW there is a problem in your code that Netbeans failed to notice. Scanner's methods do not throw IOException but supppress it. Use Scanner.ioException to check if any exception occurred during reading file.

So now we have no doubts that try-with-resources will call Scanner.close(). Now lets see Scanner.close API:

If this scanner has not yet been closed then if its underlying readable also implements the Closeable interface then the readable's close method will be invoked.

Since Scanner was created with File argument, it will create FileInputStream internally and will close it automatically. File object does not need closing since its not a Closeable resource.