I've had the same error too, it comes when you have specifyed false
path constraints on some of your IO signals.
If using Synplify Pro with the ucf constraint file, a workaround is to
use the output ndf file as the input constraint file to the PnR tool.
Indeed, the signals <signal> renamed <signalz> in the netlist are also
renamed <signalz> in the ndf file. The modifyed names are then
transparent to the PnR tool (at least in Xilinx ngdbuild, map and par).
Personnally I have written a small sed script which changes back the
names in the netlist.
Hopes this helps.