Maybe I missed it but did the O.P. have the FD-2 drive or the more common FD-1 4x4?
I have found with my FD-1 that when the engine is very cold, say below 25degrees after sitting at night, that it seems to stay at a higher rpm than normal. This seems to go away and return to normal soon after warming up while driving.
Also, no offense to the original poster, but I cannot for the life of me understand why anyone would want to use the manual mode on the shift lever. The few times I have tried it, the transmission seemed to be a bit "jerky" when it artificially slowed down or speeded up the RPM's in an attempt to shift. It really seemed like a needless wearing of driveline components for no useful purpose. If one needs more power, simply step on the gas more.....
If it were me and I felt the drivetrain was staying in too high an RPM for the load, I'd take it back to the dealer under warranty and try to talk them into a test drive with me before I'd mess with the "manual" mode.
Of course if the O.P. has the FD-2 drive, then that RPM might be normal for it but I wouldn't know as I don't have one of those.