It is always recommended that when you swap out your motherboard, you also re-install/reformat your operating system.  While there are certain circumstances that this will not be required, it is always a good idea to re-install your operating system.  When you change your motherboard, there are certain entries in the system registry that are looking for the components of the old motherboard.  If the registry does not find these components, the system can become unstable.  Admittedly, there are workarounds for these issues, but in the long run you will be better off with a re-install.  Below, is a series of links addressing this issue.

This is an overview of what happens when you swap the motherboard without reformatting your computer:

http://www.dummies.com/WileyCDA/DummiesTip/id-4723.html

Microsoft Knowledge Base articles:

This article explains why you may receive a “STOP 0x0000007B” error message after your replace the motherboard on your computer, and provides a resolution. This issue may occur if the new motherboard contains an embedded IDE controller that has a different chipset than the original motherboard.

http://support.microsoft.com/kb/316401/en-us

This article describes how to replace a motherboard on a computer that is running Microsoft Windows Server 2003, Microsoft Windows XP, or Microsoft Windows 2000. Two typical reasons for replacing a motherboard are to upgrade an existing one and to replace a failed one.

http://support.microsoft.com/kb/824125/en-us