Oligarchs ( as they call them ) in Russia got filthy rich because Yeltzin gave away basically whole country.
To compare, it is like any 40k/year Joe becoming one of the richest man on the planet in space of months because he happend to be a good friend with prime minister. If that doesn't stink, i don't know what does.
Now, Putin had two options, punish them for breaking the law ( and don't dillude yourselves thinking that they didn't ) or let them be. He choose the second - he mad them a deal - they can keep what they have, but they can't **** on his shoes as he tries to walk. This particular guy decided to crap on Putin's shoes, hence Putin started looking into how the company made cash, and suprise, suprise, it wasn't all legal.
Can't say I blame putin. Oligarchs thoughout russia's history had a thing for ****ing things up. Deal he made them was quite sweet. They couldn't sit still, so now they are - behind the bars.