This seems like a very high-level context for a fairly common problem. Being a nerd, I feel the discourse on the 64th and 86th and the pseudo-universal binary aspects of .net. But the technical troubleshooting assistant in me cannot help but think that the main problem should be simple and systematic ...
So, your real problem, regardless of the mail client (as you said yourself), and regardless of your processor, is that you cannot force the mail client to be the default protocol handler for mailto. Or it is very simple to do this, you cannot get the program that you like by default.
I tend to think that problems 64/86 problems are not relevant. They are interesting and perhaps have some kind of effect, but if the program works just fine (no problems with the code in this architecture, etc.), and if it is really just email (emails are sent and received, all SMTP and IMAP all the way), then I doubt that the OS is plotting so that the client does not become the leader of porch dogs.
In any case, I would say that the client had problems with self-esteem and is afraid to be a mailto protocol handler. Most customers cannot resist the question of whether they should be primary, and if you say yes, they pass this word along with other applications to the registry. They make sure everyone knows that they are the new king of mailboxes in the house.
So, what would I try first (basic troubleshooting): install a different email client and see if it has the same problem. If so, your OS is a bully and you will want to explore such routes.
But if this other client can get into the default program club and become the mailto handler, the problem will be in your application. This is a great wimp that does not know how to assert itself correctly.
But, like many outsiders waiting for a cool guy to take them under the wing (and wing, I mean Thunderbird. Don’t worry about any other client), your application can stand on the shoulders of a working third player, a third-party client.
We must assume that Thunderbird has performed at least one and possibly two things that your application did not do. The first is the name associated with the protocol in the registry. Go get bored and see if you can find his name and how it relates to the mailto protocol. Most likely, you can change your name to your name, or at least try to associate a protocol with you.
The second thing that T-Bird may have done was on the list of “Default Programs” (feature 7, which I didn’t like because it had a cool concept - that is, the application group, rather than waiting and seeing each if one of them can do the same job, but Windows has taken this good time (big surprise), acting like the overly protected parent he always is, and appears at the kids party and saying, “I think these two should be in this group, right? "
Ok, I hope that by accessing mailto by borrowing it from Thunderbird, you will be welcomed to the default program club, but if you didn’t, and you are still the mailto handler, I would write this at least gloat about it for a week or two before trying to solve this problem.
Now, if Thunderbird cannot get mailto control, I am very inclined to think that Windows 7, as a matter of fact, places some kind of strange caste system where the application and its installer (for example, the user) must somehow prove their worth in to be in a group, figuring out what a big secret is.
Oh, and if all else fails, try rebooting in safe mode without a network, install your client in this environment, and start it. See if you can do this by default, and the rest in paused animation. Carry out a test run (without a network, obviously) by writing a basic HTML page with mailto and see if the client opens to the client.
When you start backing up in normal mode, cross your fingers.
Let me know if any of the above issues is helpful.