I had been thinking along the same lines. I added a single day residency at Los Angeles, in transit, but that made no difference. I also checked that it did appear in the Gedcom file and that it was geocoded by FTA. I will make a cup of coffee and ponder some more.
Hmm interesting. I've emailed you via the Codeplex website, perhaps if you could email a GEDCOM extract of that one person with the single day residency file. I can invesigate why.
One thought that strikes me is if you used 2009 as the date then you have two 2009 dates and it will pick one randomly. Perhaps the only recourse is a 31st December 2008 entry to force a 2008 date to take presidence over a 1995 one.