There is no reason this shouldn't work...please /msg me if you are having problems...
Remember that win32 paths need to contain \\ instead of \... so c:\main would be c:\\main embedded in your script.
This script doesn't sleep...I wrote it to test your condition quickly.
-Jason

use File::Copy;
@dirs=qw(FullPathToDir1 FullPathToDir2  etc);
while(1){
    $dir="FullPathToMain";
    opendir(MAIN,$dir) or die "Can't open $dir:$!";
    while(defined($file = readdir MAIN)){
        next if $file =~/^\.\.?$/;
        $path=$dir.$file;
        $newdir=@dirs[$i];
        move($path,"$newdir$file") or die "move failed:$!";
        $i++;
        undef $i if ($i>$#dirs);
    }
}
[download]