In the Quartus® II software, the Cut Paths Between Unrelated Clock Domains option is turned on by default. Beginning with the Quartus II software version 6.0, this setting causes the software to ignore all setup and hold constraints on paths that cross unrelated clock domains. The Quartus II Classic Timing Analyzer reports paths crossing unrelated clock domains as unconstrained.
This reporting did not occur in previous versions of Quartus II software. To avoid these warnings, turn off Cut Paths Between Unrelated Clock Domains. To prevent timing analysis on specific paths, make an individual cut path assignment for each relevant path.