If it has the correct IP-address then it should be assigning itself to the correct site. SMS is integrated with your AD (if you have SMS 2003 that is) and based upon the subnet you've defined in your sites and services and your boundaries it will connect to the SMS server with that criteria.
Changing the SMS Client Site Code can also be done via a simple VBScript. You can then run the script manually, or deploy with SMS or GPO. Here's a sample I use and have posted on my blog (DotVBS.blogspot.com), nothing fancy. You can also use command line variables in the script to pass the site code rather than hardcode it.
----Begin VBScript----
On Error Resume Next
'Your site code goes here
siteCode = "xyz"
Dim oSMSClient
Set oSMSClient = CreateObject ("Microsoft.SMS.Client")
BOWWOW, Correct, you can use the above method to "hard code" the site code, or you can manually set it, however, you may have a bigger issue if you are atuomatically detecting the wrong site.
Is the machine in :
a) the correct physical topology with connection to the site server?
b) within the DNS Zone / IP Subnet as that defined on the primary site server.
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