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With the Radio Popper PX units, make sure the foam "doughnut" that seals between the PX receiver and the IR window on the SB-900 does not shift and block that communication. I kind of "permafied" mine, chucking the "doughnut" and using some pieces of craft foam glued to the RP bracket. Once I did that, success rate went into the high 90% rate. I also use a velcro strap to wrap around the entire SB-900/RP combo. Makes the unit very solid and still allows quick access. I'll try to post a picture of that if you're interested.
Thanks for the reminder but I've always been pretty in tune to that problem. It's looking like I my have a bad receiver. Got to call them tomorrow to see if it can be fixed.