Why is my command prompt freezing on Windows 10?

The issue ended up being a new feature of the windows 10 console. Under the default config, whenever you click on a command window in windows 10, it immediately halts the application process when it attempts to write to the console. When this happens, the command window has gone into "selection" mode.

You can tell it has happened because it will prefix the title bar of the command window with the word "Select" :

To get your program running again, you have to press escape or click somewhere else.

To get rid of this strange behavior, you can disable QuickEdit mode:

What I'd like to add here to Shaun Rowan's answer is that for it to work in all console windows you have to click "Defaults", instead of "Properties" and make your changes there, as described in this post.

I faced this problem very recently where one of the users (who had Quickedit configured on his Command Prompt) was using a tool I developed in Java, and was getting the tool frozen while running it from command prompt.

Finally what solved the problem was to redirect the logging inside the batch script to a file as shown below:

@echo off
...
java.exe -jar mytool.jar

needed to be updated to

java.exe -jar mytool.jar > log.txt