Seeing as how the UK CAA will be issuing the licence in accordance with EASA Part-FCL, the 12 month validity period of a CPL(A) Skills Test no longer appears to apply - I cannot find it anywhere (but I admit I have not gone through 1178/2011 and the Annexes in depth, only CAP 804).
Furthermore,I cannot find any reference to any requirement for a licence to have been issued within 3 years of commencement of any course. The only requirement is for the CPL(A) and IR(A) to have been issued within 36 months of the end of the month in which the last theoretical knowledge examination was sat, i.e. by the end of November 2013.
Ramin, write back to OAA and ask them for the exact references on which they are basing their statements - such statements without reference are meaningless. As far as I can see, you are perfectly entitled to apply for your ME CPL(A)/IR(A) and OAA will be required to sign the forms in the applicable sections to confirm course and skills test dates and results, etc.
As MJ states, it is up to the CAA after that and not OAA.