CodeIgniter seems to have its own method of gzipping its output (Why, I don't know, but I'm not very familiar with CI.)
According to this forum entry, such an error can occur when PHP error messages screw up the compressed content. Adjusting error_reporting to E_ALL ^ E_NOTICE
did the trick there.
Update: There also seems to be a CI config setting:
$config['compress_output'] = FALSE;
Pekka
2010-03-13 13:42:36