I've now discovered something else.
If you use the MinGW make, it will mung the command, so that it calls:
Code:
mplink ..\18F8520user.lkr w:/ m:/ FRCMapfile.map D:/msys/1.0/odefault_2005.hex ./ifi_startup.o ./ifi_utilities.o ./main.o ./printf_lib.o ./user_SerialDrv.o ./user_routines.o ./user_routines_fast.o /lD:/mcc18/lib ..\FRC_Library.lib
Cygwin's make does not exhibit this behavior.