I think the time war screwed up his sense of time and said "Body 9?((8th regeneration)) Ok, then i'll be 900!"

or

He lied. =) He probably should be 1000+ something, so maybe he's embarased about his age. ((even though old school cannon has gallifreyans being redicusly old, like a life expectansy of 10, 000))

or

Something about the time war regressed his physical/temporal age to something less than before, and he rounded around to 900.
((Remember Last of the Time Lords, how everything got sucked back to how it was before, except in the eye of the storm: the Valient. They survived, but no one else from that time frame did.
That is why he's the only surviver of the Time War. He hit the switch, did the thing that ended it, and was the only timelord in the eye of the storm.))

or

He forgot his age. Regenerations tend to screw with him pretty badly.

or

He wasn't speaking about his own timeline, but about lineral time. So in 2005, he was born on gallifrey 900 years ago.

or

Maybe he DID lie to Rose about his age, and decided to keep lieing after Rose was gone, as some sort of mourning thing. (Like the blue clothes.)

or

Maybe he thinks it's true.  His own timeline has changed before, and he was in a TIME WAR. 

or etc, etc, etc.

It is very wierd that at (the supposed start of) body 9, he would say his age was exactly 900, and at the latest christmas special, three of our Earth's and thier Earth's years later, he'd say he was 903. Who knows. Cannon in Who-verse never really stays connon, anyway.

We're talking about time travel, people! The universe could change like <i>that</i>! *snaps fingers* And it has. We just have a unique outside perspective and can actually see it happen.  Everything that we know about Doctor Who could be or has been true before, but isn't now.