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I'm always wary of alignments done with a magnetic compass. You need to have you compass probably at least 5m from the mount to eliminate any magnetic effect from the mount itself. You may get away with it if your mount is magnetically unpolarised, but leave your mount in one place for a matter of months, say, and it can be magnetised enough by the earth's magnetic field to upset your compass.
Achernar to Canopus is well within the sort of magnetic anomaly you could get by having the compass too close to a steel/metal object.
Al.
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