I rationalize it like this:
At the end of Season 2, we have the Cult of Skaro that managed to escape the Time War by hiding in the Void. When the Doctor and Rose sucked them all back into the Void, Dalek Caan did an "emergency temporal shift" and then roamed about for a while. He had some crazy time-travelly adventures of his own, through which he and Davros managed to find/make a bunch of other Daleks that also had a bunch of their own time-travelly adventures and continued to make even more Daleks.
Just because the Doctor time-locked the Time Lords and Daleks doesn't mean he's the only one who can unlock them.