Why would certain users not be able to open a mail to url from a Flash swf on my website?

You may have ActionScript problems that affect the link.

You need to ask in the Flash Professional forum.

Or, the users may not be able to see the Flash Container.

Considering the number of users these days on SmartPhones, who can't access Flash content, the worst thing you can possibly do for navigation and links is to put them in a Flash container and render them invisible to such a larg portion of your visitors.