ask your self (and your husband) this question...did your son every see "anything" happen?
when my younger brother was about 2 or 3 he walked in on my parents having sex, for a while after that my mom couldn't go anywhere w/ out him and if she left the room (like go to the bathroom or bed room) he would freak out.
so think back maybe you can remember something that might of happen that triggered his behavour.