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Cygwin is one of the packages that seems to often break when I upgrade it. In their defense, it is a large collection of packages, so presumably hard to get everything right in all circumstances. I run Debian (testing) on my Linux systems, and I rarely have any issues during upgrades. I don't know if the Debian folks are just more paranoidstrict (probably) than most, so maybe that is why I can confidently upgrade things without expecting to have to jump into the newsgroups.
Today, I upgraded cygwin, since I was going to see if clusterssh exists for cygwin, and figured I might as well upgrade first. It turns out I must have upgraded relatively recently, since the setup.exe only needed to be upgraded one minor release.
However, after the upgrade, I started getting two errors:
"bash: $'\r': command not found"
when running startxwin.sh (I use tcsh for my main shell, but this upgrade must have rewritten the startup file and so is overriding my normal shell. I'll need to fix that too, but that is more understandable on my own).
Searching around on google shows that the /etc/profile that was "upgraded" was sent in DOS format, which apparently breaks bash. So, a good old `dos2unix /etc/profile` fixed that.
I also got a "Unable to load any usable ISO8859 font" error, which turns out to be some sort of font-dependency error, where apparently, you don't get the error if you don't have any fonts except the built-in ones, but if you have some fonts installed, but not font-misc-misc, you will have issues. So, installing font-misc-misc fixed the problem, though I understand that this is a workaround until they can find a better solution.