As far as I know, cygwin tries to map windows rights to unix ones and sometimes results are very strange. Note the problem is user rights and not file attributes; read only attribute has nothing to do with it. Also, I don’t believe MEW has anything to do with it. Try some other Win32 editor and you’ll probably have the same result.
You mentioned disk crash. Is it possible you reinstalled Windows on a disk where some old files resided? Or copied files from old disk some unusual way (cygwin)? If so, old files have probably non-existent owner (previous Windows account). It may not prevent access in Windows if Everyone groups is added but can confuse CygWin. Run exploder, select one of problem files before editing, select Properties from right click menu and examine Security tab and also Advanced button. If there is something strange, delete non-existent account and take file ownership. If it is a problem, you’ll probably have to take ownership of whole directory structure. Don’t ask me how; I had to do it week or two before because we changed our domain and had similar kind of problem with CygWin. After some experimentation I was successful but already forgot exact procedure. It was far from straightforward and involved some checkboxes and buttons in exact order (user interface really improved since NT4 time when there was just one button for this purpose ).