Cannot Generate Timing Report in TimeQuest Timing Analyzer

Hi, I'm looking to investigate the setup times for a design I have. However, despite following AN 775 as best I as I can, I am not generating any outputs from my design. Instead all I see are two Data ports which I haven't declared myself in my design...

Here is the pin planner - it shows these extra pins, but also my own data ports.

Furthermore here are my declared ports in my top level file.

module bertfront(
    input clk,
    input inbitstream,
	 input [1:0] control,		//[1] start, [0] reset
    output outbitstream,
    output reg ledstatus,
    output reg [31:0] totalbits,
    output reg [31:0] incorrectbits
    );

Can anyone shed some light as to why I'm not seeing my own data ports in the timing analysis? If you need any more code I would be happy to share the entire project.