I'd guess like with the Master, the Timelords game the Doctor a extra regeneration (or more) during the Time War and John Hurt was it. The only thing that bothers me is that if Hurt's Doctor did something so bad that the Doctor is keeping his regeneration secret, then why would Tennant's Doctor keep talking about the things he had to do during the Time War?
Also, I think the Time War has been going on much longer than just between the 8th and 9th Doctor's lives. The beginning of the Time War might have been in Genesis of the Daleks when the Time Lords sent the 4th Doctor to Skaro to destroy the Daleks.
On a side note if anything I would have thought the Sontarans would have been a bigger threat to the Time Lords since they were time traveling long before the Daleks and even invaded Gallifrey in Invasion of Time.