I know what you mean. I have the same issue, and it drives me nuts. Frankly I have resolved it mostly by switching to Firefox for everything but the sites which require IE (on line virus scans, for instance, and it doesn't really work. Or FTP, which in 7 is an issue unto itself).
I think the people who developed 7 all go by the policy of "think, there must be a more difficult way to do it."
Anyway, you want an answer, not sympathy. You need to do a couple of things, which won't resolve the problem entirely. Go to your security settings and reduce them. They are still stronger than in IE 6.
Now for the trick:
Go to tools>Advanced.
*Uncheck "Warn about certificate error mismatch." (just about the last entry)
*Uncheck "Check for server certificate revocation."
*Uncheck "Check for signatures on downloaded programs" (most of the drivers I have uploaded from trusted sites for my rebuild have come in with no signature. The signature process is the reason I don't have drivers for palm..no reason to be involved in MS's bureaucracy wars.)
Now go to security settings and find the following do the following:
ENABLE the setting "Don't prompt for client certificate selection when no certificates or only one certificate exists."
(And if you don't see the stupidity in that one, you haven't been taking your vitamins.)
Dope slaps to the people who ideated the system and a pox on the house of gates, both channels.