"File.exe" is located in both folder1 and folder 2, but the App Control agent will show the file path differently depending on the physical Server OS hosting it:
Fixes to accommodate the changes made to "Fltmgr.sys" are expected in App Control agent version 8.9.2 and documented in the Release Notes. However, until agents are upgraded to 8.9.2 and higher, continue to configure Custom rules to use the physical server location rather than the DFS namespace.