This is a well-known issue in the Active Directory world. When a user authenticates in Active Directory, the first token is passed as Kerberos and then as NTLM hash. Thus any bad password actually counts as 2 strikes towards the bad password lockout number set by the domain security policy.
Microsoft recommends in mixed environments that this number be set to not less than 10. The recommendation of 3-5 is ONLY for pure Kerberos (meaning everything is a Microsoft system) environments.
There is an in-depth article here on this pehonomenon and how to troubleshoot it:
http://www.windowsecurity.com/articles/Implementing-Troubleshooting-Account-Lockout.html
There are also a number of hot fixes available to address this issue for older systems:
http://support.microsoft.com/?id=817701
I've seen this issue so many times at clients like State Farm, General Motors and the US Army Reserve that it simply isn't funny and always has been caused by security wanting the bad password count set to 3 cause that is what the lil papers all say it should be.