Machine Certificate Store in Windows 7 64 Bit.

I am running on a 64 bit Windows 7 machine.
My C# app needs a client cert placed in the "MACHINE" "Trusted Root Certification Authorities" store.
I ran this command to do this.
C:\Certificate_Automation\importpfx.exe" -f "C:\Certificate_Automation\MyCert.p12" -p "abc123" -t MACHINE -s "Trusted Root Certification Authorities"

and this command placed the cert in a brand new node in the cert store called "Trusted Root Certification Authorities". So now I have 2 "Trusted Root Certification Authorities" in the same Cert store. Bizzare. Now my application expects the cert to be in the original "Trusted Root Certification Authorities" store and doesn't see the new one.
Any idea why this is happening? Why is importpfx.exe doing this?