Two reasons
Not sure which one is the more important one.
They actually were cut loose under Yeltsin, in all practical sences of the word. Russia lost the First Chechen War. Then, one day, they decided to strike across Russian border into Dagestan, another small quasy-republic in Russian Federation. And, at about the same time, appartment buildings in Moscow and Leningrad started to blow up (that may have been a set-up by FSB, no one is sure).
So the reasons were:
1) they wouldn't leave Russia alone
2) Putin needed an enemy to look tough against. His popularity soared after he "won" the Second Chechen War.
