Hi,
if it's still interesting for you:
It seems, that you have to remove your account settings for your email provider, restart the ios device and install the email configuration again (don't forget to activate s/mime for that account).
In my case, the following params to create a new key and csr file runs perfectly in mail for mac os and iPhone/iPad:
openssl genrsa -out myKeyName.key -des3 4096
openssl req -new -key myKeyName.key -out myCsrName.csr
Then send the csr to the CA (i.e. startssl) and copy the crt-file from the CA into the directory with your key. After that, you can create the p12-file:
openssl pkcs12 -export -in nameOfCrtFile.crt -inkey myKeyName.key -out myOutFile.p12
After that, you can double click the p12-file in mac os, so that you can sign mails with Mail and you can send the p12-file to yourself and open it with the ios device (see above: remove mail settings, restart ios device, reconfigure mail setting with s/mime).
Hope it helps