I ran into the same 'issue'. My guess is that you restored a previous backup from your last iPhone. What that does is restore al your settings (minus some passwords i think) such as alarms, icon app placement etc.
When you do that it pull data from the back up file/folder in /mobile sync. I believe these backups are actually images (think .iso or .ghost) and that data is applied to your new phone. If you want to blank the lifetimer out, you can 'restore' your iPhone, and set it up as a new phone rather than pull info from a previous image. I ran into the same issue and it cleared my life timmer.
I thought it was kinda funny that only owning the 3GS for a day I had logged over 11+ Days of call time. Made it look like I owned the dam thing for a long time and was making calls on it before it was built.
Personally I think it is a flaw on the way it handles that data. Lifetime should be a reelection of THAT particular phone, and I was always under the impression that that counter could never be re-set.
just my 2 cents.
brgrds