Digital Certificates lost?

We recently began switching our clients over to IE5.5 but now are having digital certificate problems, as in they’re not there anymore and they can’t log on to secure sites like Ameritec. I have looked on microsoft support and found that these certificates can be either *.pfx *.p7b and *.sst however I cannot find any of these files on the client pc’s, are there any other files I should be looking for, where are these certificates usually stored. Major kudos for any help. Thanks peeps 8 )