What FTP client are you using - FileZilla for example?
There are retry and time out settings available in this client.
This link has some useful FileZilla network configuration help:http://wiki.filezilla-project.org/Network_Configuration
Have you tried another connection mode ie. active
(PORT) instead of passive
The link below may save you some time perhaps.
Are there any clues for your time out error in these Google Search Results
especially those results from the proFTPD forum.
There seems to be a debug log file that may give more clues - sorry, no Linux box, so not sure where to look for that file but I see links to a how to in the above proFTPD forum results.http://www.proftpd.org/docs/howto/Debugging.html
Also if you are connecting through a router then there are also tips in the above FileZilla forum results.
Make sure that it is not a firewall blocking issue that may be relevant to your connection mode mentioned above.http://slacksite.com/other/ftp.html#active
Good luck and best wishes.