ILR question/JReview - different dates from ukba

Hello All,

I need some insight into a dilemma about when to apply for ILR under Judicial review.

I initially applied to join the HSMP scheme early 2006 (can't quite remember the date). However, I have email records from back then to show that the home office sent me 3 acknowledgement emails as follows:
1. Thursday, February 16, 2006 5:17 PM - assigned me ref #: xxxxxx/01
2. Thursday, February 16, 2006 5:18 PM - assigned me ref #: yyyyyy/01
3. Monday, April 10, 2006 - assigned me ref: yyyyyy (same ref as 2 without "01")

In the 3rd email, they then stated that the application was received 10/04/06

At that time, the emails did not mean much as I had assurances that one way or the other my application had been received. It was granted and the approval letter had "May 5th 2006" date on it. Due to a severe error by the ECO, my entry application was denied and the appeal process lasted close to two years. I have since come in (2yr initial) and got an extension under JR for 3 yrs. The letter in the extension stated that my ILR date is in 2013. My questions are:

1. I know I read in the review policy that the joining date is key to determining whether one qualifies for ILR after 4 yrs under JR, and not the approval letter date or the time of 1st EC (1st visa is in 2008). However, agency who took me through the extension thinks it has to do with the time of entry into the UK(2008). Is this true, or am I correct?

2. Looking at the acknowledgement emails above (and assuming joining date is key), why did the home office send me another acknowledgement email after the law had been changed on April 03 2006 and do I have a case since I also have evidence that they have received the application before that date? Note that the ref # 3 is what they finally went with throughout my scheme.

3. Based on my story, do I have a valid case to enable me apply for ILR in 2012, or should I wait for 2013?

Sorry I could not keep it short, but please assist with your thoughts.

Thanks

BC