For previous generations of Flirc, the GUI has provided advanced configuration. The second generation of flirc uses advanced features and algorithms which render most of these configuration options meaningless. Therefore, it is normal and standard for these features to be greyed out. These options will however work for the first generation of Flirc.
In the future, some or new advanced features will be brought back into the GUI for only the second generation of Flirc. At this time, there are no options.