The following is some insight from my own personal experiences working in a large Japanese corporation in Chubu, Japan.
Please take what I say with a grain of salt as its only meant to give you a general idea of what you can experience in Japan.
When a society, like Japan, follows a strict social code, anyone who isn't aware of how to read the code and provide a sign that you understand the code, will notice some differences in how one is treated.
Don't worry though! I've had some time to learn some of this code and will share some of my insight with you in a series of entries so please subscribe and stay tuned for more.
I'll keep an index of the different topics related to this subject on a page called Social Japan.