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I'm not a Deus user, so I may be wrong on this, but I've read that the larger coil operates at different frequencies to the standard one. Possibly to reduce interference with other people using other coils.
I think it is down to manufacturing tolerances. When winding the coil, it should be x length in total but there is a tolerance of plus/minus x percent. Even a tiny difference in coil overall length of wire can give a seemingly large difference to frequency. It is not something to be concerned about and should have zero effect when using the detector.
Howard.