When using the Clock and I/O Timing dialog within Timing Analyzer, clocks that come from a dedicated input pin are not recognized. The Clock and I/O Timing dialog is accessed by selecting Analyze->Against User Specified Paths->by Defining Clock and I/O timing within Timing Analyzer.
A dedicated input pin is denoted by "IP" in the pin name; for example, IP_Lxxy_#.
Timing Analyzer does not recognize clocks that come from dedicated inputs in the Clock and I/O Timing dialog; however, when analyzing normal user-defined constraints, Timing Analyzer correctly analyzes clocks which come from dedicated inputs.
The Clock and I/O dialog is typically used to analyze the design against different clock and I/O constraints than what is defined in the UCF. If you would like to change your Clock or I/O timing constraints, you can either edit the time constrains in the PCF or edit the UCF file and re-run implementation. This will be fixed in a future design tools update.