For those interested, I did post up a similar thread over on the FJ Cruiser Forums. Those folk quickly offered confirmation late model FJ's do have marked color coded springs on the front and rear, and that mine were indeed installed backwards by the Toyota mechanics.
Finally got around to having the springs swapped back to correct sides. What a difference. Truck is level again, and even seems to drive different, in a good way. Note: dealer doubted I was right about the springs, but checked with factory (region?) and was convinced.