Are you sure you're missing data in the output? When I do this sort of thing, I include some size information in some debugging output:

my $data = ` ... `;
print "Got data length [$data]\n";
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However, if you are expecting a lot of data, you don't need to store it all in memory (unless you need it for something else). You can open a pipe and read from it. When you get a line from the pipe, you send it to the browser.

open PIPE, " ... | ";
while( <PIPE> )
    {
    ... do stuff ...
    print;
    }
close PIPE or die "Got error [$!|$?]\n";
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While debugging these things, I tend to output everything as "text/plain" so I see exactly what's going on, or I use a perl script (perhaps using WWW::Mechanize) to grab and save the output so I can inspect it later.

Good luck :)