I ran into some problems with files copied from the cygwin command line not having administrator permissions. WAMP for instance didn’t have access to these files, which is not fun.
I took this advice (found here)
As a general rule, if you are going to mix Cygwin and native tools, let windows handle file permissions ("noacl" mount option), and you'll not see such issues again.
Not sure if this is the best solution, but I added the option noacl to etc/fstab, rebooted Windows and it seems to work fine now.
# This is default anyway: none /cygdrive cygdrive binary,noacl,posix=0,user 0 0