After Much research, I figured it out. I want to post the answer here because I found others with the same problem while I was googleing, and no one had a solution. The certificates I generated were basic OpenSSL certificates that while functional, only had the bare bones. These not working certs were created with these commands:
openssl genrsa -aes-256-cbc -out odinforce.net.key 4096
openssl req -new -x509 -days 365 -key odinforce.net.key -out odinforce.net.crt
openssl genrsa -aes-256-cbc -out rhys.ferris.key 4096
openssl req -new -key rhys.ferris.key -out rhys.ferris.csr
openssl x509 -req -days 365 -in rhys.ferris.csr -CA odinforce.net.crt -CAkey odinforce.net.key -set_serial 01 -out rhys.ferris.crt
openssl req -new -key rhys.ferris.key -out rhys.ferris.csr
openssl x509 -req -days 365 -in rhys.ferris.csr -CA odinforce.net.crt -CAkey odinforce.net.key -set_serial 01 -out rhys.ferris.crt
openssl pkcs12 -export -in rhys.ferris.crt -inkey rhys.ferris.key -name "Rhys Ferris" -out rhys.ferris.p12
These certs work for encryption, but are missing one key field when it comes to iOS. You see, iOS wants to be told what the cert is to be used for, that why it says "No Valid Certificates Found." It found certificates, but none were labeled for "Email Protection."
My attempts to manually manipulate the conf file for openSSL didn't work, but I eventually found this tutorial which did. It can easily be modified for your purposes by reading through and changing the config files.
Now that my certificates are properly labeled, iOS is happy to use them.
Hope this helps!
Rhys