Module not Defined When Simulating Using Modelsim

So I've upgraded from Vivado 2015.4 to 2016.2. I use Vivado to compile the simulation files for the encrypted IPs. When I launch Modelsim 10.4, a new error appears:

sources_1/ip/output_buffer/sim/output_buffer.v(289): Module 'fifo_generator_v13_1_1' is not defined.

The first thing I noticed is that in my project flow, generated simulation files are now verilog which could be the source of my problems since I usually simulated VHDL.

First I compile the various libraries such as the fifo_generator library:

compile_simlib -simulator questa

Then I generate the simulation files:

import_files -norecurse -fileset sources_1 cgen/output_buffer/output_buffer.xci
upgrade_ip [get_ips output_buffer]
generate_target simulation [get_files output_buffer.xci]
export_simulation -simulator questa -of_objects [get_files output_buffer.xci]
exec echo exit | vsim -c -do top/top.srcs/sources_1/ip/output_buffer_sim/questa/compile.do -modelsimini modelsim.ini

My modelsim.ini file then maps these libraries:

[Library]

fifo_generator_v13_1_1 = msim/fifo_generator_v13_1_1
output_buffer = top/top.srcs/sources_1/ip/output_buffer/questa

Finally my .tcl script will build the project and add the simulation files:

vlog top/top.srcs/sources_1/ip/output_buffer/sim/output_buffer.v

Yet when I launch my project, it complains it cannot find the fifo_generator. Any ideas why this might be?

EDIT

As requested, the generated compile.do:

vlib work
vlib msim

vlib msim/xil_defaultlib
vlib msim/xpm
vlib msim/fifo_generator_v13_1_1

vmap xil_defaultlib msim/xil_defaultlib
vmap xpm msim/xpm
vmap fifo_generator_v13_1_1 msim/fifo_generator_v13_1_1

vlog -work xil_defaultlib -64 -sv \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_base.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_dpdistram.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_dprom.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_sdpram.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_spram.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_sprom.sv" \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_memory/hdl/xpm_memory_tdpram.sv" \

vcom -work xpm -64 \
"/software/CAD/Xilinx/2016.2/Vivado/2016.2/data/ip/xpm/xpm_VCOMP.vhd" \

vlog -work fifo_generator_v13_1_1 -64 \
"../../output_buffer/fifo_generator_v13_1_1/simulation/fifo_generator_vlog_beh.v" \

vcom -work fifo_generator_v13_1_1 -64 \
"../../output_buffer/fifo_generator_v13_1_1/hdl/fifo_generator_v13_1_rfs.vhd" \

vlog -work fifo_generator_v13_1_1 -64 \
"../../output_buffer/fifo_generator_v13_1_1/hdl/fifo_generator_v13_1_rfs.v" \

vlog -work xil_defaultlib -64 \
"../../output_buffer/sim/output_buffer.v" \

vlog -work xil_defaultlib "glbl.v"

It copies the modelsim.ini file and then you can run one or all three of these commands. All I want to do actually is compile so I have the object which can be used by my simulation later, which is the output_buffer.v file which is created.

# RUN_STEP: <compile>
compile()
{
  # Compile design files
  source compile.do 2>&1 | tee -a compile.log

}

# RUN_STEP: <elaborate>
elaborate()
{
  source elaborate.do 2>&1 | tee -a elaborate.log
}

# RUN_STEP: <simulate>
simulate()
{
  vsim -64 -c -do "do {simulate.do}" -l simulate.log
}

# STEP: setup
setup()
{
  case $1 in
    "-lib_map_path" )
      if [[ ($2 == "") ]]; then
        echo -e "ERROR: Simulation library directory path not specified (type \"./output_buffer.sh -help\" for more information)\n"
        exit 1
      fi
     copy_setup_file $2
    ;;
    "-reset_run" )
      reset_run
      echo -e "INFO: Simulation run files deleted.\n"
      exit 0
    ;;
    "-noclean_files" )
      # do not remove previous data
    ;;
    * )
     copy_setup_file $2
  esac

  # Add any setup/initialization commands here:-

  # <user specific commands>

}