Does the ArcGIS Server account have access to the share as well as the files in the folder? You can check these permissions if you right click the shared folder and go to Properties->Sharing->Advanced Sharing->Permissions.
Also, when you try to register the folder are you using the UNC path to that location?
Hi Vikram,
Were you able to find out the cause of your problem? I am having this same issue as you described.
Thanks
We are having the same issue in ArcGIS 10.5