This is expected behavior, and looking at the warning message shows that the problem you have is a PERIOD constraint that is also used in a number of FROM-TO constraints. Having this PERIOD constraint used in FROM-TO constraints stops the tools from propagating the PERIOD. You can resolve this by creating two TNM Groups, one used for the FROM-TO constraints and the other for the PERIOD propagation.
Please see the constraints guide for more information on the restrictions for PERIOD constraint transformation.
Conditions for Transformation:
When a TNM_NET property is traced into the CLKIN pin of a DLL, DCM, PLL, orMMCM, the TNM group and its usage are examined. The TNM is pushed through the CLKDLL, DCM, PLL, or MMCM (as described below) only if the following conditions are met:
The TNM group is used in exactly one PERIOD specification.
The TNM group is not used in any FROM-TO or OFFSET specifications.
The TNM group is not referenced in any user group definition.
If any of the above conditions are not met, the TNM is not be pushed through the CLKDLL/DCM/PLL/MMCM, and a warning message is issued. This does not prevent the TNM from tracing into other elements in the standard fashion, but if ittraces nowhere else, and is used in a specification, an error results.