the X value in the InDesign control panel , is the distance between the top left corner of the object and the 0 on the ruler.
the 6 small square in the control panel are the refrence point, which refer to which point on the object this X and Y distance would be measured, so in your screenshot
the reference is top left corner hence the distance is from 0 on the horizontal ruler to the top left corner of the object selected.
Select all the object box between which you want 6 mm seperation.
Go to Windows-->object and layout-->Align
In the Align panel...., on the bottom under "Distribute spacing" there will be two icons and a section "Use spacing"
In "Use spacing" :- enter "6 mm'
and then clikc on the button for "Distribute horizontally' --(secong one), the first icon is for "distribute vertically" and this will mess up the loyout in your case.
once done check the spacing.