On Windows 9x systems, files are always readable, and Cygwin uses the native read-only mode to determine if they are writable. Files are considered to be executable if the filename ends with .bat, .com or .exe, or if its content starts with #!. Consequently chmod can only affect the "w" mode, it silently ignores actions involving the other modes. This means that ls -l needs to open and read files. It can thus be relatively slow.
Under NT, file permissions default to the same behavior as Windows 9x but there is optional functionality in Cygwin that can make file systems behave more like on UNIX systems. This is turned on by adding the "ntea" option to the CYGWIN environment variable.
When the "ntea" feature is activated, Cygwin will start with basic permissions as determined above, but can store POSIX file permissions in NT Extended Attributes. This feature works quite well on NTFS partitions because the attributes can be stored sensibly inside the normal NTFS filesystem structure. However, on a FAT partition, NT stores extended attributes in a flat file at the root of the partition called EA DATA. SF. This file can grow to extremely large sizes if you have a large number of files on the partition in question, slowing the system to a crawl. In addition, the EA DATA. SF file can only be deleted outside of Windows because of its "in use" status. For these reasons, the use of NT Extended Attributes is off by default in Cygwin. Finally, note that specifying "ntea" in CYGWIN has no effect under Windows 9x.
Under NT, the test "[ -w filename]" is only true if filename is writable across the board, e.g. chmod +w filename.