EEA3 application with temporary NIN

Hi there,
I'm looking for some advice for my EU-partner (Greek). He has been in the UK for 6 years as of October 2014.
Oct 2008- Sept 2011- PhD studies
Sept 2011-Sept 2014-fixed term contract job
Sept 2014 onwards-permanent job
complete EHIC-avaible all years 2008-2014

Because he would like to get BC, he wants to start the application for PR. We know that he doesn't require documentation for PR (i.e. he can apply for BC directly), but as we may want to submit an EEA2 application for me next year (I'm currently on tier 4) we would like the PR document for support. We have starting calculating his qualifying period now.
While getting the documentation ready, we found that he was working on a temporary NIN for over 6 months (Sept 2011-April 2012). Because he had a university job, they assigned him a temporary NIN and he just did not get around to getting the NIN at the job centre. His P60 for April 2012 does not have any NIN and the temporary NIN is displayed in all payslips up to April 2012.
Will this gap be pulled up as breaking the qualifying period? Because in the EEA3 application form it says all payslips and P60s must feature a permanent NIN. Does anyone have any advice/experience with this?