Why are you running repackage rather than just package? Repackage does just that and re-assigns reference designators throughout the design to optimize the packaging. Package will just assign new reference designators to parts that don't have them. If you must use Repackage then try the Repackage unfixed packages and on these particular capacitors add a Frozen Package=Fix (though I'm not certain this will achieve what you want). The final option is to re-assign the reference designators in PCB and back annotate the changes to the schematic.
With the upcoming VX release, a property called Cluster can be assigned to a group of components. Components with the same value of the Cluster property will be grouped together in Layout.
For now, you can use cross probing to group components together. Select the components in xDX Designer, and they will be selected in Layout.
cluster is available in dx version also ,to group similar components in schematic and make the components connected to an ic or specific list of components to a group ,components in cluster could be placed in a single stretch