Send an EOF in Eclipse's debugger console

I just found a solution to this problem:

When you finish entering your inputs on console, click on another window (editor, Project Explorer, etc.), then click back on console. Hitting Ctrl + Z will work now.

It's a bug, see here:

Passing End of Transmission (Ctrl + D) character in Eclipse CDT console

I think it(not responding to Ctrl+D on Unix/Linux systems and not responding to Ctrl+Z on DOS?Windows systems) was a bug some 2 3 years back. Eclipse mailing lists or bugs database should have better information about it. Refer here for more info on the bug report.