I'm getting the same issues.
Just use your command line - it always works. In my case, I did a backup and restore this morning. I just backed up using the PHPBB ACP backup utility then opened a command processor (I am on NT 5.0).
- I changed to the MySQL directory on my C drive: CD MYSQL
I then ran the command processor: MYSQL
I then changed to my database:
mysql> use mydatabase
I then ran the script I had downloaded:
mysql> source c:\projects\mycoolsite\mybackup\mysite.sql
It worked great. No issues with timeouts. No reason to download the different tables.