I'd guess at the grid affecting it , but i'm sure you have ruled that out I use this free plug in from astute graphics instead, the increments size can be set as required. 1 , 10 ,100 etc And just use the arrow keys http://astutegraphics.com/software/directprefs/ Keyboard Increment Using the arrow keys on a keyboard to move, finely position and step an artwork object(s) is a common task. Normally buried in Illustrator’s extensive Preference UI, DirectPrefs makes the distance setting for this operation immediately available. With three user-definable presets for each document unit of measurement (millimetres, inches, pixels, etc.), you can switch regularly to ensure that each object is easily positioned just-so!
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