Allred began asking then-DHHR Secretary Michael Lewis if a private contractor who worked for both the state and a company that had financial stake in the contract might have used his position to try to sway the outcome.
Within weeks, Lewis decided to re-bid the contract and put procedures in place to exclude the private company from potentially benefiting from the contract.
How that was handled created a rift within the department's senior staff. The rift - between DHHR's Office of Purchasing and the department's two top lawyers, deputy secretary for legal affairs Susan Perry and general counsel Jennifer Taylor - soon became serious.
In mid-July, DHHR's new acting Secretary Rocco Fucillo put both lawyers on leave after they questioned a decision to award a separate multi-million dollar marketing contract to the highest bidder.
Now, the two lawyers and a third DHHR official are targets of an internal investigation that has been turned over to Kanawha County prosecutors.
But Taylor and Perry claim they are whistleblowers. In a lawsuit targeting Fucillo and others, the pair said the department's purchasing office has a "track record of errors" that the pair tried to correct or keep the office from making, including the MMIS problems and possible problems with the marketing contract.
The Legislative Auditor's Office eventually recommended DHHR's purchasing office be stripped of its authority to award certain contracts without going through the state Division of Purchasing. But its officials remain at work.
In August, the same legislative audit also worried DHHR has not asked would-be MMIS contractors to put up bonds in case the companies fail to deliver. Instead, the department plans to withhold a portion of payments until it is satisfied the eventual contract winner has done good work. Auditors worry this isn't enough.
Deputy Medicaid Commissioner Ed Dolly has defended the department's decision not to ask for performance bonds, saying withholding money from the eventual contractor will be more effective than having to wait until everything has gone sour to try to collect the bond.
In any event, all the attention is likely to cost DHHR the extra autonomy it has to make purchasing decisions. It is now likely to surrender those powers back to the state's main Division of Purchasing, which handles most state contracts.
It unclear when DHHR expects to announce who will win the MMIS contract.