Wish I could tell you more, but I have the same remote, and the same problem. In my case, I am trying to use the Flirc with an Ouya and XBMC. It sometimes responds, sometimes it doesn't. As for the Universal remote, I have it using the Microsoft/XBOX quick setup under the AUX button. As for the Flirc, I am using the XBMC pre-built commands.
However, I just wanted to test my Flirc, and so re-did all the XBMC commands using an old remote I had laying around (Hauppage media center remote that came with an EyeTV ATSC/NTSC tuner from many moons ago). It works without a hitch. I conclude that the problem is not in the Flirc, but in how the Universal WR7 sends its codes out. I don't think there's any way to change this. But it could be that the speed of the transmission from the WR7 is just a tad slower than the speed of a normal remote, and so the Flirc is getting tripped up. Only a hunch, and probably wrong, but an idea.
TL:DR, its probably the WR7, and not the Flirc.
