I have a system where a Virtex 6 and a Spartan 6 are daisy chained using a single JTAG connection for the programming pod. When using Chipscope the first FPGA can be configured with the net labels that were setup in the cdc file but when I use Chipscope on the the second FPGA, all I get are Dataport and Triggerport names (not the net labels that were assigned in the setup of the cdc file for the second FPGA). If I manually translate the Dataport and Triggerport signals, it does seem to trigger and display the proper waveforms. Just terribly inconvenient to have to create a manual list of signal names.
Just to reiterate, it only happens to the second FPGA of a daisy chain.