On /r/HPMOR, some have been speculating that Dumbledore coated the Philosopher's Stone with Bahl's Stupefaction, which you might remember from chapter 63:

"Bahl's Stupefaction," Moody said, naming an extremely addictive narcotic with interesting side effects on people with Slytherin tendencies; Moody had once seen an addicted Dark Wizard go to ridiculous lengths to get a victim to lay hands on a certain exact portkey, instead of just having someone toss the target a trapped Knut on their next visit to town; and after going to all that work, the addict had gone to the further effort to lay a second Portus, on the same portkey, which had, on a second touch, transported the victim back to safety. To this day, even taking the drug into account, Moody could not imagine what could have possibly been going through the man's mind at the time he had cast the second Portus.

This would explain why Voldemort let Harry keep his wand after swearing the Unbreakable Vow, and now also might explain Harry's recent actions.