Dear Dan,
thanks so much for your reply! You were right, the problem appears when the following option is checked while PEXing: "Outputs->SVDB->Generate Calibre Connectivity Interface data", and goes away if, under that very same option, I enable "Suppress pin-location information" (which has the effect of changing the, in the _calibre.rcx_ file, the entry
"MASK SVDB DIRECTORY "svdb" QUERY XRC"
to
"MASK SVDB DIRECTORY "svdb" QUERY XRC CCI NOPINLOC".
I still wonder though, what am I actually disabling by choosing the "Suppress pin-location information" option? Is this something accessory to the actual LVS/PEX operation, or it could potentially harm and make invalid my results? The documentation says little beyond the obvious; all I understood is that the CCI data is related for the integration of Calibre with other EDA tools (in particular, Virtuoso, which I am using).
Thanks again for your help.
Cheers,
Jorge.