On my linux server I run a samba share, which is used by both Linux and Windows clients on the LAN. I moved it from an old FedoraCore machine to Ubuntu a few months ago, and ever since have been getting strange permissions: text files kept becoming executable (but only for user, not group or other).
It took me this long to realize what was going on, and when I tried to track it down about a week ago I concluded it was SciTE being strange on just samba partitions. I.e. I'd edit a file with rw-r--r-- permissions, save it, and it would end up with "rwxr--r--". Every time. But not on normal partitions, and gedit didn't do it on the samba partition. I noticed today that files created by a PHP script also got those weird permissions, and the penny dropped: gedit must be explicitly setting permissions when it saves a file. Scite wasn't the cause of the problem at all.
So, I went hunting again. I referred to Mount samba shares with utf8 encoding using cifs a lot, but in fact it didn't give me the answer I wanted: the instructions there gave me the same problem. (It did show me how to set my samba partition to mount from /etc/fstab, replacing my crude entry in rc.local though.)
Hunting through the troubleshooting section I found the "nounix" flag and tried that. Initially it made things worse, giving all files rwxrwxrwx permissions. Then I changed from "file_mode=0777,dir_mode=0777" to "file_mode=0644,dir_mode=0755" (which was what I had originally), and that combined with nounix works! All text files are rw-r--r-- before and after saving. Oh, the other change I added relative to the above page was including "uid=darren,gid=darren". Otherwise files were owned by "nobody:root" and I didn't have permission to edit anything (even with the suggested 0777 settings).
My guess is that my old FedoraCore samba server didn't have the unix extensions, Ubuntu 8 does, and somehow those unix extensions are misconfigured in Ubuntu. My samba server configuration is all defaults however... Anyway, it now works the way it has for the previous few years, so I'm happy.
UPDATE: I just realized this has also fixed another irritation - delete (that moves to the Trash folder) hasn't been working on that partition, but now it does. Trash folder vs. direct delete was only a minor factor; what was really annoying was every time I pressed delete it then popped up a dialog box requiring me to confirm it.