Beyond TV 3.5 Expressvu 6100 (Echostar 801) and USB-UIRT

I was using an SA 3100 cable box in this configuration without issue and then changed to the Expressvu/Echostar DSS box and now I am having problems with the USB-UIRT. BeyondTV 3.5 simply won't control the box...even after I have programmed the channels on the "learn" remote page. It accepts them, but in testing it doesn't function. So...I tried using Girder to program more of the remote features, and it learns the commands, but when I try to run them against the box nothing happens. I am wondering if there are additional elements that I need to adjust beyond the defaults and where should I start (threshold, fequency etc). I am also wondering if it is possible that the IR remote is sending something unique to the DSS box that would prevent me from using a univeral remote to control it....not sure how this would be possible....but thought I would ask.
Also, I was hoping to use 2 USB-UIRTs on the same system and tie them together with Girder. I have the server/HTPC in the basement rack and along with the amp and DSS/cable boxes and one USB-UIRT is installed there. I also have a USB hub in the media room on my main floor where I would like to connect the second to enable the use of a remote to control the projector and system players such as BeyondTV 3.5. Is there a way that I can route specific Grider commands to individual USB-UIRTs?
Also, I was hoping to use 2 USB-UIRTs on the same system and tie them together with Girder. I have the server/HTPC in the basement rack and along with the amp and DSS/cable boxes and one USB-UIRT is installed there. I also have a USB hub in the media room on my main floor where I would like to connect the second to enable the use of a remote to control the projector and system players such as BeyondTV 3.5. Is there a way that I can route specific Grider commands to individual USB-UIRTs?