well having the exact same issues with a raspberry pi and using flirc with a Samsung remote it works fine after I plugged it in the first time, but as soon as I do a reboot it does a double key press again.
I used:
Raspberry Pi
Samsung remote
Flirc V1 with 0.96 program version
XBMC setup
I did the record twice thing but it doesn't seem to do the trick.
It would be a nice option if you could add a keystroke delay in the program so it gets stored in the module hopefully that could solve the problems.