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That's definitely a software fault. What it sounds like it's doing is computing Alpha, then when you go to try an alignment on Canopus, the software then seems to think the telescope should be pointing north, so it takes 180 degrees off the alt-az for Canopus and slews the scope around to that point. It's almost like it suddenly forgets where its pointing and then decides it should slew to the north. Try aligning with northern stars only and see what happens. If it aligns OK, then there's something buggy with it recognising the Sth Hemisphere. But if it does the same thing as before, then it must be getting north and south mixed up.
What I'd do is get the firmware previous to the version you now have, wipe the controller chip clean and install the old version, then add the latest version of the firmware, skipping the version that's in there, now. It's obviously screwy to the point of being nearly unusable.
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