It sounds like you aren't getting everything cleaned out to me. Additionally you need to make sure to change your access passwords. If you can't determine how they initially got in then change them all for that domain.
What kind of site is it a Content Management System? a Shopping cart?
If CMS what software Joomla, WP, other?
If Shopping cart what cart software?
You may want to do a virus scan on your home computer.
A little more info would be helpful.