Room impulse response 'noise'
First of al it's a very exciting idea to capture a room's impulse response. Hence congratulations on your challenges. Assuming that you have correctly implemented the software he provided in his page, then the only cause of the differences are; (Note: I can say nothing about his method of computing the RIR. It can be a proper method or not... Only the possible cause of differences you observe I'll discuss)

1- Speakers: He uses monitor quality Yamaha speakers, you use crappy PC speakers (just like mine or yours; they are all crappy when compared to a Yamaha monitor speaker)

2- Microphones: He uses high fidelity, high linearity, low noise, high sensitivity microphones , you use web-cam crappy microphone. (again we all use those PC microphnes but they are crappy compared to any professional one)

3- Speaker and microphone placement: it's very vital that you place the speakers and the microphones to the correct places, otherwise you will be measure something that you don't want or need to.

4- Room: His impulse response is from a church. Your's is from a living room. When compared to such a structure, so you should be measuring different room impulse reponses of course.

However, even the most interesting part is, how and why do you judge your impulse response from its graphical plot appearance? You should judge it from its acoustical result point of view. 

Have you tried your calculated room impulse response to add a reverb effect to dry audio, to see if it works? i.e.,to see if the dry audio becomes as if it was played and recorded in that room you refer to its impulse response? 

You should do this test with a head-set ! otherwise you would be applying the room impulse response twice when played back in the same room...