Unusual Situation-Foreign National

Hello All, I wasn’t sure to post this in FSO subsection but thought this is where I can get the best answer. And for all those who comment just for the sake of commenting, please save your breath i.e. talking down to people and/or condescending tone etc.

I am in the Army Reserves and came to my unit in Spring 2016. My unit requires TS. At the time I was in the process of marrying my foreign national fiancé whom I met through family. The fiancé lived in a different country at the time. I notified my leadership that I will be marrying a foreign national and plan to bring them to the states as quickly as possible. My unit leadership advised that I might not be able to obtain TS clearance if I went through with the marriage. I called off my marriage and decided to proceed with the SF-86. I completed the SF-86 in May 2016 and listed the ex-fiancé as a foreign contact. I also put down on the SF-86 that I was going to marry this foreign national but decided against it due to the concerns my leadership had.
In June 2016, I had my one and only interview with the BI. I brought up my foreign national contact and how I called the marriage off. The BI stated that marrying a foreign national will have no bearing my TS application. They explained how adjudicator looks at the whole picture concept. I told them in that case please note that I plan on marrying my fiancé (if they and their family will agree to it).
In Spring 2017, I traveled overseas to marry my fiancé. Before my travel, I emailed my HR SGT and gave them the required online training for overseas travels as well in the same email I updated that I am flying overseas to marry my foreign national fiancé. My HR SGT did not have any questions for me(My TS was still pending at this time).
After my return from overseas I added my now spouse as my dependent. They were added to my life insurance policy and were eligible for other Army benefits. I also obtained an immigration letter from my HR SGT that I am in the Army Reserves to provide to the USCIS with my spouse’s green card application in order to expedite our case.
In early fall, I traveled overseas to meet my spouse as evidence that I was in a bonafide marriage. This was to provide USCIS per their request for proof of marriage.
In late Fall 2017, my TS was finally adjudicated.
In Summer 2018, my spouse’s green card application was approved.
In Winter 2018, I traveled overseas for the final wedding ceremony. My spouse and I flew back together and they have been living in the US as a permanent resident since then.
I went away last week for a training course and during the first day the course instructors asked our class if anyone had a foreign spouse. I raised my hand along with two other classmates. After reviewing our records I was removed from the course be cause my spouse information was not in JPAS. The schoolhouse had me complete an SF-86C on my spouse and ask if I had proof that I notified my unit about my marriage. I provided them the email from Spring 2017 that my unit was tracking this a well as the immigration letter they typed up to provide to my immigration lawyer and the immigration services. The unit never asked to complete an SF-86C.
Meanwhile, my unit pulled my DOD SCI while they investigate this.
My purpose to post this here is to find out what will be the next stop. How negatively will this impact me? I was up front about all of this as well I notified my unit each time I traveled overseas. I added my spouse to all my Army records so they could be in the books. I want to know how best handle this?
Thanks to everyone in advance.

Based on what you have told us here, this sounds like a paperwork snafu. My experience has been that Reserve/Guard has not been very good about entering things into JPAS and keeping up with reporting requirements like the civilian sector. My civilian employers always knew more about the security clearance process. Also, most States outsource the security clearance process to the main HQ which is responsible for the entire State. So the customer service may not be the best.

Good luck

Do you know if my clearance will be pulled completely or will they just update my info ie input my spouses data into JPAS? Also, should I let my civilian job FSO know as well since the civilian side tends to work quicker?

I would definitely do that

I spoke with my assistant FSO at my job they recommended to let the Army process the SF86C forms. However, they also said they can update JPAS with my spouses information. My reserve unit FSO said that I can access back to the army SCI by having my Commander sign off on an acceptance of risk memo. My CO already agreed to this seeing how I’ve been upfront and honest since day 1.