At this time using copy and paste to copy a group of footprints or symbols will not paste the objects with the reference designators in the same order as the original set.
Example: if there are 8 diodes, D1 thru D8 that are copied-pasted they should be sequentially numbered D9 thru D16. The software currently randomly renumbers the string.
I have reported this issue to our developer and we will fix this in the future.
You can right click on a footprint and select properties. On the Component tab you can change the reference designator.