Obfuscating email set by global variable
It might be that you're trying to parse the variables within quotes " as you set email so you're actually encoding {{ emailContact.emailField }} as a string, not the value it represents. Something like this should work:

{% set email = "&lt;a href='mailto:" ~ emailContact.emailField ~ "'&gt;" ~ emailContact.emailField ~ "&lt;/a&gt;" %}

{{ email|rot13 }}