The JTA has more detail on Chabad's "Chief Rabbi of Russia," Berel Lazar's citizenship issues.
It seems Putin gave Lazar special citizenship in 2000, opening the door for Chabad a few days later to make Lazar "Chief Rabbi of Russia," in a bid to force out Putin critic Vladimir Gussinsky and the real chief rabbi, Adolph Shayevitch.
Very recently, Lazar has for the first time been mildly critical of the Putin regime's weak response to antisemitic incidents, including a knife attack at a Chabad synagogue that wounded nine Jews, some very seriously. This "citizenship inquiry" may be retaliation for Lazar's belated and weak attempt to speak up.
Look for Putin to "save" Lazar from this "trouble" and Lazar to extoll the virtues of Putin. Otherwise, expect Lazar to spend some time in New York or Israel on an enforced "vacation," like Moscow's Chief Rabbi, Pinkhas Goldschmidt.