Tier 1 General Route
Initial application: Employment + Self-Employment (2011 however tax amendments /payments made 2016 March)
Extension: Employment + Self-Employment (2013 , Tax paid on time however HMRC records not updated so
HMRC made amendments along with my 2011 returns).
ILR application: Employment only.
Myself and my dependent (wife) went to Croydon during 1st week of May 2016, with all the required documents, visa office call me told me that your HMRC records are not same as you mentioned in your last 2 application with home office, I filled that self-employment form and submitted the letters from HMRC and my updated SA302 for 2013. And I told visa officer that HMRC currently working on 2011 return and that also going to be updated accordingly. I submitted the tax returns/payments for the year 2011.
Visa officer came back after 3 hours with a refusal and told me to ask my current company to arrange a
Tier-2 visa or I may have a option to go through AR. Visa office return all my wife documents+ refusal letters however hold couple of my original documents (tax, my MSc degree , Life in UK test, employment letters).
I came back home with disappointment and very next day I talked to one of the solicitor as he has done couple of complicated cases (tax issues/employment issues etc) and one my friend refer me to talk to him, I sent my refusal letter and he recommended me to send a new application with limited documents as my original documents with AR team. So I sent my/dependant both applications again before my expiry date in May. In the month of June I received my biometric however home office lost my wife application and sent her biometric in July. During that period I contacted HMRC (compliance team) to expedite my request for updating my 2011 tax records and they updated my records in July 2016.
First week of August I received an email from home office that they haven’t received my wife passport, I forwarded that email to my solicitor and from that point my solicitor get in contact with the visa officer and explained him my current/previous situation.
Last week of August 2016, visa officer approved my application and sent all the documents + biometric to my solicitor.
One advice to everybody, its really painful process to be very honest but don’t lose your hopes and stay positive and then all will be good.
Solicitor is always good in order to deal with complicated applications as this is all about the game of impression nothing much

Hope this info helps you!!