Sounds like this: link text
From the limited information you posted, I can almost guarantee that you're running some sort of open-source software on that site--Maybe not on the exact site that's affected, but there's probably some on the server....and it's also not likely patched up to current standards. I've seen it happen with phpBB, Joomla (especially Joomla) phpMyAdmin, and Wordpress. It's almost scary common and 99% of the time is nowhere near as sophisticated as many think it might be. It happened to me on a very old test install of Mambo and at work with a rogue install of phpBB that someone on the IT staff snuck on the server to communicate with their fantasy football league.
Thing is, hackers are lazy. Unless you've got something they really want, there's no reason for them to go and hack you individually...it's not worth their time. However, if you're running a common piece of code with an exploitable codebase, they can scan sites for it at random, and when they find the hole, attack automatically. Hence the reason the code will be identical in content and location nearly all the time.
Park the site...put up a "under construction" page. Pull your code down and scrub it, whether by hand or automated. Now stop! Update all open source code, no matter how recent it might be. Now do sanity checks on permissions, SQL queries (especially search boxes that aren't escaped) and user permission systems. Run Script injection tests. Finally, once it's all cleared to the best of your ability, test, test, test. Finally, thought it likely had little to do with the problem, change your password and use a good password strategy to protect it.
Good luck. Be careful!