I can't confirm that:

perl -le "system('start /min cmd.exe')"
# starts a minimized command window, just as expected
# This is perl, v5.8.5 built for MSWin32-x86-multi-thread
[download]

So maybe show us your code - you get bonus points if you can reduce it to the following four lines:

my $cmd = "..."; # this is the important part you have to supply
print "Trying to launch '$cmd'\n";
system($cmd) == 0
    or warn "Couldn't launch '$cmd': $!/$?";
[download]