Which is the value of '$fop'? ...

open (POO, "logfile") or die "Can't open logfile: $!";
my $FOP = "fop -xsl $XSL -xml $XML -pdf $PDF |";
print POO $FOP;
open (HUH, $FOP) or die "Can't run fop: $!";
while (<HUH>) {
    print POO $_;
}
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maybe you must put the entire path to the 'fop' program.