To work around the problem, find the PLL Quartus II IP File (.qip) file and expand the PLL instance names fully.
For example:
Change the following statements in .qip from:
set_instance_assignment -name PLL_COMPENSATION_MODE NORMAL -to "*cpui_serial_pll_0002*|altera_pll:altera_pll_i*|*"
set_instance_assignment -name PLL_AUTO_RESET OFF -to "*cpui_serial_pll_0002*|altera_pll:altera_pll_i*|*"
set_instance_assignment -name PLL_BANDWIDTH_PRESET HIGH -to "*cpui_serial_pll_0002*|altera_pll:altera_pll_i*|*"
to:
set_instance_assignment -name PLL_COMPENSATION_MODE NORMAL -to "cpui_top:cpui_top|cpui_serial:sbus|cpui_serial_pll:rx_pll|cpui_serial_pll_0002:cpui_serial_pll_inst|altera_pll:altera_pll_i"
set_instance_assignment -name PLL_AUTO_RESET OFF -to "cpui_top:cpui_top|cpui_serial:sbus|cpui_serial_pll:rx_pll|cpui_serial_pll_0002:cpui_serial_pll_inst|altera_pll:altera_pll_i"
set_instance_assignment -name PLL_BANDWIDTH_PRESET HIGH -to "cpui_top:cpui_top|cpui_serial:sbus|cpui_serial_pll:rx_pll|cpui_serial_pll_0002:cpui_serial_pll_inst|altera_pll:altera_pll_i"
This problem is fixed beginning with Quartus II software version 13.1.