Thank you for your answer, I figured out why, GZIP is insalled on my machine by the way, it's that when setting ob_gzhandler, the buffer is compressed chunk by chunk, so when using ob_get_contents(), parts of the last chunck are missing, and I end up getting weird output.
To correct that behaviour (or at least to bypass it), open a second output buffer, and leave the one with gzhandler() alone.
Like this
ob_start("ob_gzhandler");
ob_start();
Now the second one isn't compressed, I can do whatever I want with it (hence get its content, clean it etc). The content will be compressed anyway given that a higher level output buffer with gzhandler is opened.