Can you copy paste the entire exception message that you are getting, this has limited information and with this it is difficult to see what the problem is.

Some time back i had prepared a PDF doc for setting up iFolder with AD, that had instructions to import certificate from AD. I guess you will find that doc in this forum some where, i remember some one had uploaded that.

The problem is Mono's certificate handling in a more complex setup. I get an -2146762490, which indicates that the purpose of the certificate is wrong, the problem is, that the certificate that's first checked in the chain is the one from the Intermediate CA (We've got a Root CA -> Intermediate CA -> Certificate) which can only sign new certificates for certain purposes. So, accepting the certificate in the setup has no effect, because of the certificate chain an the certificate options. Regenerating is no option, because the CA is deployed everywhere and works perfectly in all of our setups. So, maybe there's a trick in mono to trust all certificates, because placing the certificates in the Lookups has no effect, because of the Problem.

Yes you are absolutely right about this problem, here is a way to correct the same(if some one else is interested, using self signed certificates).

https://bugzilla.novell.com/show_bug.cgi?id=518402

Above bug captures lot details regarding the  -2146762490 issue and details about how to verify your certificates with openssl for other problems etc... In fact also has  a workaround to solve the same.

Above solution probably might not be of any use to you, as you have no plans change the certificate chain. There is a way to ignore certificate complexities with code change(accept all certificates) and still support SSL(but that is going to be a hack and security violation so not recommended) , so as of now we have no plans to support that.

let us see, in future if we do come up with some answer for this,  we will try and share that info with all of you.