Did you set the start bit on the FP module? Open labview, target the FP module. Go to Tools -> Network: Options -> RT Target Miscellaneous and confirm that 'Launch Application at Bootup' is checked.
Also on that screen confirm that:
Application Path = c:\ni-rt\startup\startup.exe
Downloaded vi Path = c:\ni-rt\startup
Lastly, ftp to the FP module and confirm that c:\ni-rt\startup\startup.exe exists and has a correct timestamp.
Matt