Input Ports don´t show up in Timequest

Thanks Rysc for the reply, yeah looks like there are getting synthesized out. I placed some logic and attached a clock to it and it now appears in the list.

I didn´t see any messages in the processing window of Quartus saying it was doing this. I ran a few tests on another program I had using timequest and the input pins I checked that were not used in the design were still available.

I´m not sure what critera Quartus uses to remove the input pins from the design, but anyway it seems in this case there is no serious problem.