Comment 2 for bug 240294

Update, I was partially wrong. The issue occurs when you do a checkout with tortoise bzr, then use "bzr status" (or commit etc..) from cygwin is when it believes that the file permissions were deliberately changed. It does not seem to be an issue when you branch with command line bzr from cygwin! Also - if you branch with tortoise bzr - before you do any work, use cygwin, go to your working directory, run "bzr revert". You will not lose any work (as you have done none) and it will put the working tree in a state that matches the repository - and TortoiseBzr appears to continue working as desired.

This really only applies to those who wish to use command line and ui interfaces for bzr..