We went through a similar thing a few years back with SSL certificates.

GoDaddy offered super-cheap (relatively speaking) certs, but none of the major browsers had GoDaddy in their default list of certification entities at that time.

So the upshot of using a GoDaddy cert was that every visitor would get a "not trusted" warning, even though the cert was legitimate.

That's not something you want your users to see when they're in the middle of signing up or downloading something from your site.

I don't know whether or not this concept applies to java & jar too, but you might want to confirm it before making a decision.