Thanks.....I keep forgetting about the tcl commands showing up within Quartus II and TimeQuest. I prefer to use these tcl commands, albeit with a more readable clock name, than just using a single command.
I've found that in order to completely understand which PLL output is attached to which signal name in the schematic, I need to refer back to SOPC Builder. For example, pll.c0 is <pll_instance_name>.clk[0], and from SOPC Builder, you can see which clock name was used whenever the PLL wizard was used. Why TimeQuest doesn't use these clock names for the -name option, I don't know.
I agree that it's a little unusual to see the -source option used that way. If I traced this in the Verilog generated netlist, I would probably find that this signal is coming from the input clock pad or the output of boundary scan cells or some other input pad test logic.
Thanks again for the heads up on the tcl commands.
Tony