Lewis,
I have the MX-850 + the MRF-250. I had been using the 850 as an RF line of sight remote for several months before hooking up the MRF-250. I initially had issues with the IR use. I finally dicovered the various settings in the software under the "Program" menu, "RF Setup". After tweeking with them. I believe I set them all to "IR & RF" and having the flasher settings on the right "line" or jack position in the rear of the MRF-250, AND playing with the flasher position on the 990 front panel - things finally began working remotely. Hope this helps-if you haven't already solved the problem another way.
Live from Maine, waiting for the snow!
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990, 7500, Pioneer DV-45A, Boston Acoustic (BA) VR-M90 Fronts, BA VR-920 Cntr., BA PV-1000 Sub, BA VR-MX Surrounds, Pioneer Elite Kuro Pro 151-FD Plasma, Panamax MAX 5100-EX, Salamander Rack.