I have an ssh/sftp remote connection that otherwise seems to work fine. It can launch terminals, browse the folder tree etc etc.
However, if I either drag an executable file into the remote file tree (from the local one) or I set up a "C/C++ Remote Application" which downloads the binary first it will copy the file ok, but fail to set the permission bits (defaults everything back to 644).
If I then log in and manually set the permission bits to 755, it then runs fine.
I don't know if this is also meaningful, but the error message from eclipse when it tries to run this c/c++ remote application is a file upload error (nothing explicit).
Scp/sftp'ing directly from my host to the embedded board doesn't have this problem.