BruteForce is 1990...
Check ALL sites running on your server. Make sure there isnt any type of backdoor. Look out for last modified files. Shells (backdoors) can look like .jpg .gif and so on. So they are pretty tough to spot lately. Also check all your applications running on your server for the latest exploits.
If you want to talk more detailed, hook me up on icq. Iam always here to help
