The original crimes he plead guilty to in 2015 and was sentenced (money laundering, obstruction of justice). This new crime he plead guilty to a few months ago and was sentenced this week (money laundering).
The new crime is that after he had plead guilty in the 2015 case he was out on bond awaiting sentencing. During that time he took a backup of the Bitcoin private key for the 1,600 Bitcoin the USG had seized from him and moved them to an offshore account.
The USG went to sell or move the Bitcoin they had seized from Bridges and found all of the addresses empty
He was caught (again) and plead guilty (again) - and this time handed over all of his keys and hardware wallet and returned the 1,000 (on a hardware wallet) + 600 (in a market account) coins
As an aside - the obstruction of justice charge is insane. In his first theft, he transferred some coins to a personal MtGox account. He later learned that the USG was investigating MtGox and knew that eventually they would discover his MtGox account if it was seized. So he transferred his MtGox coin out and then sent them a seizure notice so that they would be tipped off to the investigation.
It had its intended affect - the DOJ called off its investigation into MtGox (this was mentioned in sentencing memo)
Ars do a good summary of the new charges and some of the other aspects of the case:
https://arstechnica.com/tech-policy/2016/07/corrupt-agent-wh...
edit: To add, we don't get many technical details of this case because of the plea - but i'm curious to know for certain how they traced the second theft back to Bridges and how they found his new Bitfinex account. It isn't hard to believe they always suspected he had taken them, and then worked backwards looking at his movement etc. - but for now we can mostly only speculate
Here is what we do know. A day before he was supposed to hand himself in, he was raided and they found id documents, offshore corporate records, a new passport, citizenship applications for his wife for a third country, a macbook with serial number filed off, etc. Its likely they subpoenaed bitcoin markets for those offshore entity names. It also looked like he was going to run:
http://ia601308.us.archive.org/17/items/gov.uscourts.cand.28...