It's a bit confusing, can you set out exactly with the dates
1) when you first moved to the UK;
2) when you started exercising treaty rights, apart from the first three months' stay initially;
3) WHERE did you get married (here or abroad in Lithuania)
4) when your husband moved to the UK
5) The WAY you exercised treaty rights in the UK (working, self-employed, student, self-sufficient);
6) The documents you provided with your EEA3 application;
7) When you applied for WRS Scheme;

When you completed 5 years of exercising treaty rights;
9) when you applied for Doc certifying your PR;
For your hubby to have acquired PR automatically there are certain requirements:
a) he must have lived in the UK IN ACCORDANCE with the regulations (i.e. married to you while you were exercising treaty rights IN THE UK) for 5 years (disregarding! periods of absences of up to 6 months PER YEAR).
That is why I asked when your hubby first came to the UK, so that you can count 5 years from that time;
b) YOU must have been exercising treaty rights for 5 years, while he is here, as when applying for PR, he will be basing his application on this fact, there will be more info requried about you than him;
thus, the fact that you were advised by UKBA that he is only eligible upon the end of that period is strange, to say the least. I'll explain why it doesn't make sense:
1) for you to have acquired BC, you needed a minimum of 5 years' exercising treaty rights (that INCLUDES the first year under WRS as well) + 1 year on the status of PR. If we deduct 6 years from Nov' 2010, that's Nov' 2004. However, we also have to deduct a couple of months for processing your Naturalisation application (let's say 2-3 months) and to process your EEA3 application (another 1-3 months). So, you have been probably exercising treaty rights and entered the UK with the first Accession of Lithuania back in 2004?
2) That means, for you to legally have got a PR, you had to have been exercising treaty rights and complying with EU law throughout this period at least, this is the earliest anyone from the new Accession states could have acquired BC, apart from the ones who married a Brit themselves and thus saved a year;
3) the fact could have been that your hubby, as you said, had already been in the UK on some other visa (student, work even illegally! but that does NOT MATTER) when you met and got married in Dec'2005;
4) the UKBA staff back in 2005/2006/2007 and even now, are ignorant of the law, and having seen your hubby switch his status, took ages to process the application and even advised him wrongly on the time to apply for PR.
Please confirm that the above assumptions are correct, I cannot see otherwise.
Thus, if YOU were eligible for PR some time in 2009, provided your hubby stayed with you for at least 5 years from your marriage in the UK and did not enter some time later, you SHOULD apply on form EEA4 immediately without any fuss or anything.
Don't worry about the 15 days between 14 Nov 2010 & 1 Dec 2010 (5 years' anniversary), as you said, you must RENOUNCE your nationality... to lose it. For the UKBA you will be for the purposes of your hubby's application a Lithuanian with PR applying for her hubby. No need to leave the UK etc, the caseworker may just check if your passport/id card is valid, declared lost/stolen or is counterfeit.
Unless you contacted Lithuanian embassy, they will confirm, if contacted (I don't see why they could be contacted) that the passport is valid, not declared lost/stolen etc, so all will turn down on:
1) the proof available to your husband of him living in the UK for 5 years without breaks of longer than 6 months per year;
2) Proving relationship- marriage certificate from 2005;
3) proving you have been exercising treaty rights for the five years he is claiming; You can provide a PR document, and for the peace of mind, all the documents you provided initially when applying on form EEA3 yourself (WRS card & certificate) etc. to make it complete and not let them ask for more info;
Post all that to Liverpool and off you go, happy days. Once your hubby gets his PR card, he can immediately apply for BC himself, on the basis of being married to YOU- a british citizen. All is not that bad, after all, you could have him neuteralised

by the end of this year (6 months max for PR application and 3-5 months at most for naturalisation application).
Please keep us up to date with the news.
ladyd wrote:
We got married in 1 dec 05 and I got naturalised 14 nov 10!
I was not aware that my country has not supported dual nat and that this whole situation would have got us into a such pickle! Talk about terrible legal advice!!
We may think about just applying on EEA first and then see from then on.
But I thought that because I had to complete 5+1 , one year worker reg scheme and then start excersizing treaty rights. At the time of our marriage I imported my Wrs in august 06 and my husband had limited leave to remain till Oct 06. They gave him first stamp in july 06, them second one residence permit as a family member few months later. Latter stamp is expiring on 10 nov 11. , this is the date ukba advised us to apply for permanent residence.
Sounds a bit complicated! Sorry, typing on a small screen doesn't help.