Are you using Expect? You don't say which modules you are using.

If (as it seems) you are using Expect or the module you are using is using Expect: The expect.pm documentation for version 1.15 (and also 1.21) which is a bit sparse on some details uses $fh->send("y\n"); to send responses in the examples provided. Don't know if that makes a difference though

Also there is a debug method you can call on the Expect object. Called with a parameter of 1, 2 or 3 you should get more information about what is happening.