mplink errors in eclipse

I tried using eclipse ide for code development. But I get a funny error during the mplink step. I tried the same mplink command from a shell and that works fine. Why does eclipse cause this problem?

Here’s the build error from eclipse.

Building target: BallBot_2008.hex
Invoking: MPLINK Linker
mplink “…\18F8722.lkr” /a INHX32 /w /m FRCMapfile.map /o"BallBot_2008.hex" ./ifi_startup.o ./ifi_utilities.o ./main.o ./user_SerialDrv.o ./user_routines.o ./user_routines_fast.o /l"C:\mcc18\lib" …\FRC_library_8722.lib
MPLINK 3.90, Linker
Copyright © 2004 Microchip Technology Inc.
Error - unrecognized input: C:/msys/1.0/a
Errors : 1

make: *** [BallBot_2008.hex] Error 1

My environment is eclipse on Windows XP.
I saw the same problem after installing msys (in order to get the rm command to fix the “clean” problem with eclipse) I uninstalled msys and switched to GnuWin32. Everything is fine now.