Hi Bhargava,
Have you checked in the file content that the files are really the same?, at least in the X first bytes because one files are bigger than the others with the same name.
If it worked in the past is a really weird thing, i think something in the application or whatever to deposit the files originally have changed its functionality and it seems they are duplicating the files. If the business logic doesn't need to have the IDOCs in real time, i would suggest to do an ATP to pick the files in a determinate period of time and to talk with the responsible to generate the files in order to avoid to share the same time. In this way, you can check if the files are really the same (with the same size and data) or not.
On the other way, you should implement a code to avoid the duplicity and i think right this must be your last choice.
Regards.