I have also found that you must thoroughly clean any area that has been "marked". Depending on the type of bedding you use, you might want to consider dry cleaning them (it does help). If you can wash it separately and put some enzymatic cleaner in with the wash. (I use OxyClean and it works like a charm.)

You might also consider steam cleaning the carpet in the bedroom, maybe he is picking up on a scent and trying to mask it

Good luck, I had the same problem with one of my cats and it took me months before we finally resolved it.