When a component or group is scaled, there are options that activate in the right click context menu, for groups, the ability to “reset scale”, for components “reset scale” and “scale definition”.
“reset scale” returns the object to its original size. “scale definition” resets the size to the present scale, so if the component has been scaled to 1.5, then “scale definition” will replace the component with this new size (scale now 1) and any other instances will be a factor of this new definition
When creating nested components or groups it is possible to include some that have been scaled differently and others with none. This is the same for DCs, creating an odd box then imputing values to overwrite the grayed ones creates a scaled instance. I believe out of sync parts to a DC can cause issues though this behaviour seems hard to predict, so for safe modelling I try to build DCs with known values, match results to the grey,
So in the fix I find a sub components original size, using “reset scale”, undo then set the value to the original, then match all the rest. Maybe this is not necessary as one can force the sizes with the formula, but I feel much more at ease if everything is in sync.
I can not tell how the geometry became displaced, probably with your attempts to fix the DC by changing the raw geometry, which has caused more problems