The patch provided at https://github.com/phpmyadmin/phpmyadmin/commit/5298602f8edb4475fce5d299532c7780e0e314a5.patch, and merged in 4.0.6, causes mod_deflate enabled servers to double-gzip-compress the exports again.
Commenting out the following in export.php returns single compression behavior.
4.0.5 with patch applied at server
4.0.6 first upstream merged release
4.0.7 upstream merged release
Add deflate detection when PMA_Responce::getInstance() is bypassed, if possible.