Firstly, can you confirm that you are operating via a limited company, as you do not explicitly say so in your original post.
My understanding was if all employees are paid under the LEL then there is no requirement to register for PAYE.
The strict position is that in the absence of a P45 issued by a previous employer the employer offers the employee a P46. You would have ticked it to say that you were in receipt of a pension, which would have triggered the use of tax code BR - basic rate 20%. So there was a PAYE failure in terms of a loss of tax at the time that the first salary payment was made. It doesn't matter whether it would have all been sorted out at the year end (i.e. that your personal allowance would have covered the salary). The PAYE regulations / employer guidelines are clear.
The 2010-11 employer returns (P14, P35 etc) should have been submitted by 19 May 2011.