When a disk is formatted with a FAT format (as used on PCs) then the Mac will create DS_store files to store information such as icons, file comments and so on that the Mac HFS filesystem stores as part of what is called the "Resource Fork".
The .DS_Store files contain the view preference settings for the folder they are contained in. They are created by OS X whenever you change or set the view and options for a directory or directly access a folder that does not already have a .DS_Store file. In OS X any file name that begins with a "." is invisible so you do not see these files on your Mac, but they are there. Windows, on the other hand, knows nothing about invisible file names beginning with a "." so they show up there.
There are utilities that will delete these files on a Windows server, but the only way to keep them off of the server is to never access the folder from a Mac running OS X. Which, of course, defeats the purpose completely.