FIXED!
Stupid wiring in the car, from before I had it (either done in Japan, or in AU after compliance). The ground lead was hooked to the anteanna signal lead on my headunit, and the ground lead was lying around and I had been trying to hook the antenna signal from the HU to it.
Hence it had been playing silly buggers with the antenna, amp and other things turning them on, off... up down, left right... whatever.
I had assumed this wiring was all right as the headunit had been working fine and was wired the same as the older toyota AU spec headunit it had when I bought it.
Anyway, radio on... CD player, antenna stays down. Switch to radio mode, antenna goes up. Switch back to CD mode antenna goes down
It so fucking huge tho, sticks up over 2ft above the roof-line of the car when fully extended!