Edit: The link provided above may cause issues, as it's for the R3 release and SF is still using the R2 boards. There's some new features with the R3 and I don't know how it will behave when trying to save it to an R2 board. You can find the files for the SC2-R2 on the "
Downloads" page of the NEC site (in the right-hand column), rather than the page for the board.
The saber should be wired as RGBA order. The problem is that the voice menu and PC config edit program are set as BGRA order for the Spark Color 2 - R2.
Are you using the in-hilt voice menu "Spark Colorset Editor" to do this, or are you using the PC program "Spark Color Config Editor"? (which I believe the install files are included on the SD card)
If it's the voice menu, you will just have to deal with it and remember that "red" is actually "blue" and vice-versa. On the PC program you can go to Options > Color Settings and change the order temporarily. You will need to do that every time you use it though, if you want an accurate preview in the "Spark-ulator".
I just downloaded the SC2-R3 (new update as of a month ago) software onto my work PC and it seems to be defaulted to the proper RGB order now; can't confirm the voice menu though. No idea when SF will run out of their R2 versions and start stocking the R3.