My wife (non-EEA national) and I (UK citizen) are preparing to make an application for her SET(M) ILR at the moment and I have found that we lack documents in her or our names for the first 2 months after she arrived in the UK.
We successfully applied for a spouse visa outside UK and my wife traveled to UK 10 days after being granted the visa. At the time we had no knowledge about ILR rules, we were just relieved to have got the spouse visa with just one return interview!
My wife arrived at the start of Dec 06 and stayed with my parents for one month while I finished out a work contract in her country. She was meant to find accommodation for us both, instead found she was pregnant, and became over-whelmed, so she returned to where I was just before New Year. 3 weeks later we both returned to UK to stay with my parents again until finding our own accommodation.
Because of this we do not have any official documents except her passport stamp to indicate her time here during December/January and my concern is that by a strict interpretation of the rules, my wife and I have not been 'living together under one roof' in UK for the full 2 years.
We were married for 1 year before she came to UK and I was her sponsor for the spouse visa. Annoyingly I no longer have the work contract from that period because I wasn't thinking straight during a recycling binge, so it's difficult for me to prove what I was doing

I have asked my parents to provide a letter stating that they gave us accommodation during that period, and I have got several personal bank statements addressed to me which cover that period sent to my parents address.
As we now have plenty of evidence of living together for the remaining period, from February onwards, plus our lovely little baby, I'm confident that the rest of our case is solid.
My question is:
Will the PEO at our appointment want to know that I was out of the UK when my wife arrived on her spouse visa and will it detriment her application? Will they look at my passport entry dates and will they want proof of what I was doing at that time?
How important are joint letters which are dated the first few months and will a letter from my parents suffice to cover this lack? Considering that we have alot of documentation afterwords and a 16 month old baby, would they be likely to give us the benefit of the doubt?
Sorry for the waffly post, I hope I've made my question clear and given you guys enough info to answer.