Modelsim + Cyclone V PLL = Error occurred in protected context

It seems that cyclone V VHDL library has some problem. You can get through the issue with using verilog library instead, but PLL reconfiguration model looks to assume VHDL library. Can you try as follows?

(1) compile both VHDL and Verilog library

vlog %QDIR%\eda\sim_lib\cyclonev_atoms.v -work cyclonev_ver

vcom %QDIR%\eda\sim_lib\cyclonev_atoms.vhd -work cyclonev

vcom %QDIR%\eda\sim_lib\cyclonev_components.vhd -work cyclonev

(2) refer both VHDL and Verilog library in vsim

vsim -do "do wave.do;run -all" -novopt -t ps -L work -L altera -L lpm -L sgate -L altera_mf -L altera_lnsim -l cyclonev_ver -l cyclonev work.tb

** You should refer "cyclonev_ver" before "cyclone"