I've temporarily adopted a solution... Since i know a little about C# programming, i've written a simple application. It basically runs at startup and looks for XMBC windows instances to automatically change send the keyboard layout change command to XBMC.
It's not the perfect solution, but since we don't have the possibility to change Flirc's keyb. layout, it works fine for me. I hope the programmer will include features like this in future releases, it would be cool!
:)