This seems very similar to an issue I have had. Please try the latest release of Calibre xRC.
If this does not fix the issue, please submit a Service Request on SupportNet so we can assist you in detail.
I have resolved this problem. I did make sure I was using the latest release but that did not help. The problem was in the cellmap file provided with the design kit. that has capital letters for D S G B when the terminals that Calibre is looking for to assign net name are all lower case. We copied over the cellmap file and changed all the cases of the terminals and net names were assigned correctly.I don't know if there is a more automatic way to accomplish this but this is what we did to make it work.