My version:

#! perl -sw
use strict;

my $pos = tell DATA;
my %tally; ++$tally{ $_ } for map split( '&' ), <DATA>;
my $lines = $.;
seek DATA, $pos, 0;

print join '&', grep{ $tally{ $_ } != $lines } split '&' while <DATA>

__DATA__
a=1&b=1&c=1&d=2&e=&f=3
a=1&b=2&c=3&d=2&e=&f=4
a=1&b=2&c=5&d=1&e=&f=5
[download]

Produces:

C:\test>junk
b=1&c=1&d=2&f=3
b=2&c=3&d=2&f=4
b=2&c=5&d=1&f=5
[download]

For a real file, you wouldn't need the tell, just rewind the file with seek $fh, 0, 0; for the second pass.