It could also be that you are sampling the pulses at different times. The output of a remote control is modulated on a carrier of around 482Khz. Therefore, you want to be sampling the input at this frequency to get data will look the same between successive samples. Your BJT circuit will suffice, after all, all you need is an amplifier to make it a logic on/off. I am not sure of the output of the detector, but you may need a schmitt trigger to make sure that the logic transitions are fast enough to be within spec of the logic type you are using.

Learning remotes may sample at a higher rate, i.e. 800Khz for arguments sake to make sure that they can cope with remotes that use different frequencies. When you then push the button for the programmed function, it then plays back the samples at the sampled frequencies.