Pydio recommends to disable the output buffering of PHP for improved performances. When doing a fresh install, you should get the following message:
you should disable php output_buffering for better performances with pydio.
In order to do that on Debian using Apache2:
In /etc/php5/apache2/php.ini find this line:
output_buffering = 4096
And replace it by:
output_buffering = Off