Sometimes we can see the same certificates in certificates store. Why this is like that? There are various stores are available for certificates. Logical store, Physical store and also we can see the certificate purpose view.

1.MMC->Certificate->View->Option



2. You can change the store view



3. Certificate Purpose View




When we see the logical view ; we can see the same certificate in the certificate store. Why that is like that? That is for combine of physical and logical store. For more info see http://technet.microsoft.com/en-us/library/cc757166(v=ws.10).aspx
You can verify that  by comparing the serial numbers. How to comparing the Certificate serial number?

Also you can see the link for comparing the Certificate Serial numbers.
http://blogs.technet.com/b/yuridiogenes/archive/2011/04/20/exporting-certificates-using-certutil.aspx