First a question back: Are you really using a second IR LED to detect the IR light? Does that work? I only know the schematics with a IR detector (photo transistor) but would be interested to get the details how to do that with an LED. Do you have a link to more information?
To your problem: is the whole system within a closed box? If not, you might get some refraction from air temperature differences between the emitter and the receptor.
To be able to use the signal on a digital input you have to amplify it before feeding it into the Arduino.