How to fix SQL Server instances with different builds on same server? I have a Windows 2008 box and there are 5 instances of SQL Server 2008 Standard installed. 

After that, SQL Server service pack patched. 

Weird thing is: the builds for those instance are different. For example, 


One instance build No is 10.0.5512.0  
Another instance build No is 10.0.5500.0 


Confused. When applied SP on the server, this patch should be for all instances on this server. 

How could this happen? How to fix it?
Sounds like someone applied a security update, but only selected one of the instances to apply the update (or it was installed prior to the instance at 5500 was installed). 

To fix it, you can run the update again (5512 is from a security update I blogged about here). It should give you the option of which instances to apply; check all that you can. The ones that are already at that patch level (or higher!) will be greyed out.

In fact, I recommend you apply the most recent cumulative update, Cumulative Update #15.