I'm not a lawyer or an expert, but I think my statement explains why funds held by Silk Road were confiscated and not returned to their owners. In the U.S., your property can be confiscated if it is involved in crime whether you are involved in the crime or not. Maybe banks are a special case and maybe not, or maybe it would be political suicide to confiscate the assets of a bank so it isn't done.
The United States successfully convinced a federal judge that the Silk Road bitcoins are traceable to criminal activity, simply through the bitcoins’ presence on a site associated with the transacting of illegal goods.
What the government did there is a civil forfeiture. In a civil forfeiture the "defendant" is the property - i.e. the bitcoins. The government only needs probable cause to execute the seizure of the bitcoins. Then any person who wants to make a claim against the coins must file as an interested party. I do not know, but seriously doubt, anyone filed as an interested party in an effort to get their coins back. Those coins seized were ones seized ON silk road as opposed to ones that had already left the market place. Civil forfeiture has a much lesser burden. Probable cause to seize but the the burden is on the government to show by preponderance of the evidence the funds are connected to criminal activity should someone claim an interest in the property. However most of the time no one claims an interest and as in that case the government just wins by default.