It looks like a generalized situation all across the board. I hold MRPT with HHS and I am switching to State Dept due to a new job. I require the same MRPT from State to start my new job. Since State does not accept clearance from other USG agencies, the contracting agency has to do my clearance from scratch. I submitted by eQIP in December and fingerprints were received 01/03/2017. I was informed last month that my interim clearance is denied. However, HHS gave me interim clearance within 30 days (this was back in 2014 when things were relatively fast) and my full MRPT clearance finished in 6 months. These days it seems to take 5 months just to get to the point of interim clearance. I hear from many hiring managers that denial of interim clearance seems to be the norm these days.
The most frustrating part of the process is the lack of information. I kow for sure that none of my country contacts have been approached yet (I am based at a US mission abroad at the moment) and the person who does clearances at the US embassy has not received any information about me. It's been 6 months and nothing seems to be moving and there is no information from any source. Meanwhile, I am separated from family because of this clearance process and it is only adding to the stress. I guess that is part of the course. Fortunately, I am able to continue to in my current job with HHS.
I understand I am not alone in this frustration and delays. I hope sharing our experiences will result in some consolation and lessen the stress.