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One quick question - are you using a compass to get the polar scope axis initially NEAR True South (Mag South MINUS mag declination seeing you are Melbourne)? If you use a compass or mobile phone app,make sure it is at LEAST a metre away from the mount (I solidly mount a good compass in an aluminium bar attached to the head) otherwise they will be afflicted by the magnetic influence of the mounts motors, circuitry etc.
I had been aligning pretty spot on for ages. Moved it to my dark courtyard, and CONSISTENTLY 11° out in azimuth - no matter WHAT I tried, including a new motor board! And you know what it was? Steel reinforcement / rebar in the slab underneath me, couple with the steel house frame and steel roof etc etc etc I was SURROUNDED by magnetic fields, causing all mayhem with the compass and mobile phone app (which are pretty dodgy anyway in my experience)!
Also, which version of the Synscan software are you using? The latest version is USELESS for Southern Hemisphere realignment - sends incorrect adjustments (it sends you the WRONG way). 3.27 is the last semi-usable Synscan software. DO NOT USE THE LATEST RELEASE!
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