Some of the companies building the system opposed an early decision by the Medicare agency to use database software from a company called MarkLogic, which handles data differently from systems by companies like IBM and Oracle. Some suggest that its unfamiliar nature slowed their work. By mid-November, more than six weeks after the rollout, the MarkLogic database — essentially the website’s virtual filing cabinet and index — continued to perform below expectations, according to one person who works in the command center. In interviews, MarkLogic’s executives faulted inadequate computing power and instability at the site’s data center, as well as the failure to properly integrate their product, problems repeatedly cited by other website vendors.