Sorry for the delay in getting back to you. I recreated this configuration on my local machine today and was able to see the problem. When I investigated the code I found there is already a solution for this built in but it wasn't documented anywhere. I guess it hasn't come up much because most people who use an SSL certificate do install it as a root level site.
If you add this to your user.config file it should solve the problem
<add key="IsRunningInRootSite" value="false" />
Note that you'll need to touch the Web.config file after that because it won't automatically detect changes in user.config.
I've added a note about this to the section about SSL on the Securing mojoPortal article.
Hope that helps,