Did you try to check your certificate with openSSL? See the how to here: https://www.sslshopper.com/article-most-common-openssl-commands.html If openSSL says the certificate is ok, file a support ticket.
Regards,
Ronald
The system in the Mendix Cloud only works with one client certficate per pkcs12 container. With some help from the openssl tool you could split your file into two pkcs12 files and upload them both individually