You never know what strangenesses can develop when software package features start interacting. I'm trying out the latest joe release (3.1) on the latest Cygwin release (1.5.10-3), which I have running on Windows XP pro SP1. I have my Hard Disk Drive formatted NTFS, with compression enabled. On NTFS, each file is compressed separately; the "switch" to turn compression on or off is implemented as a file attribute. Compression of an entire drive is accomplished by setting the drive attribute, which is then inherited by all directories and files created or modified on it-- unless, I suppose, a process explicitly changes it.
Thus far, this system has worked flawlessly for me, including with all previous versions of joe that I have built and run on previous Cygwin versions. But the current joe on the current Cygwin saves files with the compression attribute turned off. No other Cygwin utility does that, and neither did the previous joe (2.9.8). I have no guess as to where to even begin to look for a solution. :(
"...unless, I suppose, a process explicitly changes it."
That is to say, unless a process explicitly changes the attribute of the file(s) it is saving or modifying.
"...and neither did the previous joe (2.9.8)"
I take that back-- it does. So it's a Cygwin problem. I'll have to see if any other Cygwin apps do this.