Could it be they have no chance of getting the one system to work they have decided it would be "better" to leave data in a couple of (existing) databases.
According to the BBC article:
The government has reportedly spent about £35m on IT consultants since the ID cards project began in 2004.
I really should have gone in for that. Trouble is, I don't think they'd be able to pay me enough to compensate me for the emotional damage of working for the government on something that is a fucking stupid idea in the first place.
With any luck the good people at No2ID will have their way soon enough.