>& redirects both stdout and stderr on some shells. time prints its output to stderr (this is useful because it allows you to redirect the program's stdout and just see the time info, but that's besides the point). You could try:
system("time $RUNHOME/$jobfile > $RUNHOME/gcp_${FilName}_${total}.gs.out 2>&1 &") which should redirect both stdout and stderr to the $RUNHOME/gcp_${FilName}_${total}.gs.out file.

Update Wow, must be smoking too much crack, I suggested the exact same thing that tye did and didn't even realize it.