How Can Vim and Windows See Two Different Files that Have the Same Name in the Program Files Directory

As Raymond Chen and @kreemoweet pointed out above, this is caused by filesystem virtualization. To turn this off, you can use the Local Group Policy editor, gpedit.msc. Type start gpedit.msc into a command prompt and navigate to Computer Configuration > Windows Settings > Security Settings > Local Policies > Security Options. Scroll to the bottom of the right-hand window and double-click on User Account Control: Virtualize file and registry write failures to per-user locations. Change the setting from Enabled to Disabled.