SharePoint 2010 Version History Issue

We have this issue going on for one of our users for quite some time.He is uploading a document to a document librrary which is versioning enabled through a script or batch file.When he uploads the document 2nd time to the document library and goes to the version history page of the item he sees that the date and time stamp of the previous version has been overwritten with the date and time stamp of the current version.Has anyone faced this issue before.If yes please share youe experiences and any resolution to the same.The scenario can be best described by this post http://ift.tt/1tJHeJG .The only difference between our scenario and this scenario is that in our case the time stamp is exactly the same as that of the previous version.