Multiple Customers having Problems with .pem files -chain certificate

I have 2 different customers who recently started using weblogic. My Applications are ASP hosted web services and require digital certificates. For added security, our CSO uses a chain certificate. The private cert is signed by an intermediary verisign cert which is signed by the Root CA. 
Embaressingly, I just found out one Customer completed side-stepped the BEA implementation for .pem files and implemented a non BEA class to work around based on difficulty they had trying to get the .pem file for the intermediary verisign cert to work. I am stuck in that I don't want to advise the second client to do the same thing, but I can't find great support on what to do and some of the BLOGS are conflicting. From what I understand, this first client struggled on this for 2 weeks and gave up. What I am trying to ascertain is whether the private .pem file is suppossed to have both the RSA PRIVATE KEY as well as the CERTIFICATE of the intermediate cert inside that one .pem file or not. I can see their needs to be a .pem for the intermediary and a .pem for the private but not sure if any of the data should repeat.

Also, good samples of how these should look would help. The .pem files my client showed me looked incorrect.

Please note both these clients are top Investment Banks and I think it's in both Bea's interest and my interest to see this work on Weblogic without coding around the default Weblogic security implementation.

Hi Patrick,
If you fixed the issue changing your PowerShell code, would you mind posting the working code here for reference for other people that might experience this problem?
Thanks in advance.
Nico Martens - MCTS, MCITP
SharePoint Infrastructure Consultant / Trainer

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Multiple Customers having Problems with .pem files -chain certificate

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