I see...
If the problem is purely timeout, you can try manipulating the limit:
In phpMyAdmin's
config.inc.php, there is a config var called
$cfg['ExecTimeLimit']. You can set this to 0 (zero), which means infinite (up to the PHP's max excution time).
Open your php.ini and find
max_excution_time and change the value to whatever the value (in seconds) you think would be sufficient for phpMyAdmin to finish excution. You may also want to check
mysql.connect_timeout.
If you do not have access to your php.ini, I think these directives can be set via ini_set() on runtime, too:
PHP: ini_set - Manual
http://ca3.php.net/ini_set
I hope this time it's useful.