The reason for this are the process configuration.
1. Project Configuration --> Configuration Data --> Planning --> Plan Attributes: The Complexity attributes might be set to Estimates. The progress editor is supposed to work with the Enumerations and numeric attributes, not with the Duration Attributes for the Plan Elements. That is the reason why the progress is shown in the milliseconds and not converted to hours and days as it is in the estimates column.
Solution for this: Usually the Complexity is used in the Agile Planning than the traditional. The out of box formal template does not have any attribute set as the complexity attribute. Currently there is no way to clear the complexity attribute from the UI. If you really want to use the complexity for estimation then it can set this to some valid customer attribute similar to the story points in Scrum template.
2.  Project Configuration --> Configuration Data --> Planning --> Work Item Type Categorization: the work items types for which the wrong progress is shown might be set as the plan Element than the Execution element. This is the reason why the progress is calculated using the complexity attribute instead on the Estimate attribute.
Solution for this:Just un-check the work items types for which the wrong progress is shown as the plan element.