managing certificates through registry or GPO (remove local CA certificates from list)

Hi

we use our identity card (Belgian Citizan CA) to sign our pdf documents, so they can be viewed and trusted outside our organisation.

Our local domain CA integrated it's own certificates in the digital ID list in Acrobat Reader. People can now select this certificate and sign documents, but this signature is only valid inside our own organisation.
Is there a way to manage the list of certificates that can be chosen from in Acrobat Reader? registry wise of script wise? Where is this 'list' stored? It seems like all the user cert's are imported (mmc.exe->cert)

All check boxes in "windows integration" are unchecked.

thanks