You may run into an unusual issue when running virtualized sequence of Cygwin under App-V. The app will sequence correctly and launch both during Monitoring phase and Launch phase, however when you attempt to launch app in any deployment context you'll get error:
Resolution: There're two ways to successfully sequence Cygwin:
Prior to Sequencing, create an exclusion for Sequencing Drive and Cygwin home directory. If you're sequencing to Q:, you would add in following path: Q:\cygwin.001\cygwin\home. This assumes you're sequencing to Cygwin.001 as the mount and the install directory is Q:\c ygwin.001\cygwin).
If you want to modify package, you'll need to Edit the package and under files, change attributes for Q:\<MNT>\Cygwin\home path to de=select override and change type to "User Data."