If your are using BAM API to update the values of the BAM milestones and the hours registered are wrong  , this can be caused by the UTC of the machine the query is running on . To fix this try not to use System.DateTime.Now but System.DateTime.UtcNow.

Example:

Microsoft.BizTalk.Bam.EventObservation.OrchestrationEventStream.UpdateActivity(“MyActivity”, myActivityInstance,”milestone”,System.DateTime.UtcNow);