I had the same issue.
My replacement glass doesn't have "that little piece that separates the ambient light and the prox". So i used the idea from [http://www.ifixit.com/Answers/View/55630/iPhone+4+proximity+sensor+not+working+after+replacing+BLACK+GSM#answer56563|Simon's method] but instead of using electrical tape i used the black marker, painted on the glass similarly as it done on the original Apple glass. Did it several times so no light come through painted area. After that sensor's windows on replacement glass looks almost exactly as on original glass, and proximity sensor began to work.