You will see this message if you create your own Qsys project using an Avalon®-ST variant of the PCI® Express Hard IP core and do not include the Altera® example application (Titled "APPS" in the Altera created example designs), and do not drive the pld_core_ready signal on the Hard IP instantiation.
The full set of messages look like this:
# FATAL: <sim time> Current Link Speed is Unsupported
# FAILURE: Simulation stopped due to Fatal error!
Drive the pld_core_ready signal on the Hard IP core instantiation to 1\'b1.