The solution

This won't be very interesting or useful to anyone except other developers I'm afraid but I thought it was worth a quick blog post to help others. Essentially I was reading a remote gz file using gzread and streaming it into a local file;

while (!gzeof ($in_file)) {
   $buffer = gzread ($in_file, 4096);
   fwrite ($out_file, $buffer, 4096);
}

But that was just getting stuck in a loop for some reason. I have to say I didn't ever work out why (bug in my coding or bug in PHP), but I did find a workaround by using this method instead:

while ($line = gzgets($zh,1024)) {
   fwrite($fc,$line);
}

Other web developers beware! Hope this helps.