I just received my FLIRC yesterday and it looks like this might be the problem I am having as well. I'm running Windows 7 and trying to use my Vizio TV remote to control WMC. It is doing really screwy things. I've forced upgrade to the latest firmware, enabled the sequencing check box in the advanced settings and nothing has worked.
When I tried programming the WMC remote, none of the more complex shortcuts like skip forward skip backward worked at all. When I manually mapped these shortcuts in the full keyboard, screwy things would happen in WMC. For instance, skip forward works for the first keypress, and then it starts sending all sorts of weird things like numbers and all sorts of other commands. It is as if maybe the CTRL or ALT key is sticking or something.
I tried clicking on the link that Jason provided to read the comments in the RC forum, but I don't have permission to see that forum. Will this update be released soon... will it resolve this screwy behavior in WMC?