Three weeks after MF Global's collapse, furious former customers are still fighting for access to billions of dollars as they question why as much as two-thirds of their money is still frozen.

While authorities have touted the fact that they are returning 60 percent of the collateral and cash that had been frozen in the wake of the broker's October 31 bankruptcy, a closer look shows that in fact only about 40 percent of customers' total funds have been authorized for release so far.

The remainder, more than $3 billion, ostensibly remains on hand to cover a shortfall originally estimated by MF Global to regulators at just $600 million.

Because the bankruptcy trustee, regulators and exchanges have made no comment on the missing funds in weeks -- and have given no information as to how much cash they are retaining -- customers are left guessing exactly how much might end up in the creditors' process of the bankruptcy.

After weeks of intense lobbying by customers and exchanges, trustee James Giddens last week won court approval to release another $520 million in funds from MF Global accounts that contained only cash as of October 31.

But that has still left thousands of customers in an uproar. Clients who had a mix of cash and trading positions have yet to see a dime of their excess funds, they say. The trustee is planning a third cash transfer to cover these clients, but no timing for that tranche has been announced.

The whole process is a mess, said Jason Skole, a private investor who had invested $200,000 at the start of this year in a small hedge fund who traded through MF Global.

Those who had just cash positions will get some of their money. All I've got is 60 percent of the small amount of collateral I had backing trades, he said. He says around $185,000 of his money is still frozen at the bankrupt firm.

MONEY TRAIL

The tale of the customer's funds goes like this. On October 31, exchange operator CME Group estimated in a court filing that there was a requirement of some $5.5 billion in segregated customer funds -- including, presumably, the missing funds that could not be immediately located.

Over the following weeks, while authorities poured over sloppy and haphazard records, the trustee identified two pools of money that could be partly returned to customers.

The first was $2.5 billion in collateral that was being used as margin to cover existing trades. Those trading positions were transferred to new brokers along with 60 percent of the value of the collateral, or about $1.55 billion.

The second was $869 million that was left in MF Global accounts that contained nothing but cash -- either because customers had liquidated all their trades before October 31, or because they simply had no positions open as it failed. The bankruptcy court ruled last week that those account holders would also get back 60 percent, or about $520 million.

Those two pools of funds only account for about $3.4 billion of the original total $5.5 billion. The customers whose accounts hold that remaining $2-plus billion have never been explicitly identified, or told when they will get their funds.

It's clear that some cash is being held back in order to cover the missing money that regulators say MF Global may have taken from customer accounts, an unprecedented violation of one of the fundamental tenets of commodity brokers.

What has not been clear is why officials have declined to be more specific about how much money they believe should be in those accounts, regardless of what is missing.

...The Trustee should publish a report showing how much funds have been accounted for, how much has been distributed and how much he is still holding, said Ronald Filler, director of the Center on Financial Services Law at New York Law School.

Once the accounting nears completion, one would hope that another 20 percent or more will soon be distributed, leaving an adequate amount to cushion any shortfall. If the Trustee holds on to the remaining 40 percent without explanation, then one could possibly presume that the shortfall may be greater than $600 million. Let's hope not.

One answer became clearer on Friday: Some, perhaps most, of those unexplained funds are being held by customers who had both open trades and large sums of money on account at the stricken brokerage, ex-MF Global customers said. While these customers have been reunited with their open trades, their cash is still frozen.

The result? More than $3.3 billion or 60 percent of total customer funds at the time of the bankruptcy are still frozen.

Kent Jarrell, a spokesman for bankruptcy trustee James Giddens, said in a statement they were working on a third bulk transfer to true up the value of distributions so that all former customers get 60 percent of their net equity, but said they could not guarantee all customers would be made whole.

At present, the assets the Trustee has control of in commodities segregation are substantially less than the estimated allowed commodities claims, Jarrell said.

There is no assurance of a 100 percent return.

CME Group referred all questions to the trustee.

MOUNTING ANGER

While customers were initially outraged at the thought that MF Global had tapped into their segregated funds, that rage has increasingly been targeted at the trustee and the bankruptcy court for the handling of an unprecedented collapse.

The (bankruptcy) Trustee is creating new protected classes within a pool of segregated customer assets, said John Roe, a spokesman for the Commodity Customer Coalition, a group lobbying for the speedy release of funds representing 7,000 former MF Global customers.

(This) has dangerous implications in future Future Commission Merchant (FCM) bankruptcies. How is this in the interests of customers, FCMs, bankruptcy creditors or the system as a whole?

It is still unclear what happened to the $600 million of customer funds unaccounted for since MF Global's Chapter 11 filing, and whether MF Global might have illegally mixed customer funds with its own or used them for its own proprietary trading.

The Commodity Futures Trading Commission, federal prosecutors and the Securities and Exchange Commission are all investigating the bankruptcy.

(Additional reporting by Nick Brown in New York; editing by Marguerita Choy, Jonathan Leff and Edward Tobin)