Citizenship Timing - in country 3 years prior

Timeline:
18-Aug-06, left UK for 3 weeks.

11-Aug-09, applied for Citizenship via NCS Center.  They told me that the Home Office would recieve my application on 14-Aug-09.

18-Aug-09, letter confirming payment is dated for this date.
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If the Home Office recieved my application on 14-Aug, but didn't take payment out until 18-Aug, which date do they use as "start" date?  Because if it's 18-Aug, I'm screwed b/c I was out of the country 3 years prior.

There is no hidden complication here. The received date is the date they received it ... in your case 14th August. The post room date stamp applications as soon as they are opened.

So no problem for you.