It seems stupid but I got it fixed, I opened the pem file and saved crt and key files separately and that worked like a charm. Here are the instructions from Ask F5 that I used. I never had to do this before and all my microsoft cert formats used to work without having to separate the crt and key files. Any ways, I am all set.
Using a text editor, divide the new PEM-encoded file into separate certificate and private key files by performing the following procedure:
1. Cut the text beginning with BEGIN CERTIFICATE and ending with END CERTIFICATE, making sure to include the BEGIN CERTIFICATE and END CERTIFICATE statements.
2. Save the certificate text as a new text file with a .crt extension.
For example: mynewcert.crt
3. Cut the text beginning with BEGIN RSA PRIVATE KEY and ending with END RSA PRIVATE KEY, making sure to include the BEGIN RSA PRIVATE KEY and END RSA PRIVATE KEY statements.
4. Save the key text as a new text file with a .key extension.
For example: mynewkey.key