You missed part of the output. Notice you have
That 1.0e+03 means that the part displayed below all has to be multiplied by 1000 to get the actual numbers. So for the -0.0001 entry displayed, the real value stored is roughly -0.1 -- with -0.1250 being entirely consistent with that possibility.
I recommend that you stop using "format short" and start using "format short g" or "format long g"
There is a Preference you can set to change the default output format.
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