Java Card, Web Start and 2 certificates

I have a WebStart application that is required to use client certificates. These certificates come from a user's Smart Card that gets put into Internet Explorer. WebStart will automatically grab the certificate and send it to the server.
My problem comes when there are 2 certificates that fit the profile. In that case, a dialog pops up asking the user to pick 1. It comes up with just about every new connection made back to the server.
The way I see it, my options are:
1) Try to reuse connections, extend keep-alive so not too many connections are made.
2) Try to get the certificates from Internet Explorer manually and pass one of them with the connection
or
3) Read the certificate directly from the Card and pass it along.
I've been trying #1 for a while now, and it doesn't get too much better.
Any ideas?

I'll have to check. I'm not running the system, so I don't have any control over this.
If it is, should I grab it out of there?
I'm sorry, Java Card and certificate programming is new to me, so...
The code required to grab the certificate out of the Microsoft Certificate Store would be OS-dependent? If I grab the certificate directly off the card, would that be OS-independent?
Is this true?

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