Hello,
step to reproduce

install windows server 2012 standard ( NOT R2  i see no problem with R2 )
install latest cygwin 64 bit from cygwin site

you can run some program like ls.exe or other from command promtp with no
warning

C:\cygwin64\bin\ls.exe

update microsoft windows , after installing june 2021 security update
kb5003697

every cygwin command that you run from command prompt you have this warning

Cygwin WARNING:  Couldn't compute FAST_CWD pointer.  This typically occurs
if you're using  an older Cygwin version on a newer Windows.  Please update
to the latest  available Cygwin version from https://cygwin.com/.  If the
problem persists,  please see https://cygwin.com/problems.html

i see no warning with other microsoft windows version and no problem with
cygwin 32 bit .

if i uninstall

kb5003697

and reboot we have no more warning but we can't install this security fix

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