I'm with you there -- I find Cygwin starts slow and unstable, and then seems to rot at an astonishing speed, to the point where it's usually unusable after I've had it installed for a couple of months.
Cygwin doesn't rot. It doesn't automatically update, and nor does it self-configure, so there's nothing to cause the rot. I've never had problems like you describe.
The biggest problem - and what I suspect is happening to you - is when you have third-party programs and utilities that interfere with Cygwin, most often by putting an older or newer version of cygwin1.dll on the $PATH (i.e. you may be using Cygwin as part of some other program and not be aware of it). Cygwin uses shared memory; multiple versions of cygwin1.dll disagree on the format of this shared memory, and things go pear-shaped pretty quickly from there.
Also some antivirus programs can trip up Cygwin; in its emulation, it sometimes has cause to open, close then open files in quick succession, but AV programs sometimes analyse files when they are opened by programs, and cause bogus timing-dependent sharing errors.
I love Cygwin, but I have experienced what I would describe as rot. (manifested via errors on fork()). I think that's caused by things changing around it, via windows dll updates, but I don't have a lot of insight into windows' dll handling and whatnot so I don't know for sure. Also pretty sure installing new cygwin packages can cause this. Usually, rebaseall fixes such problems.
In any event, I much prefer Cygwin to the alternatives.
The rot tends to set in as I install packages to Cygwin; the more I add, the slower and less stable Cygwin seems to become, to the point of taking tens of seconds to reach a prompt after opening. Make of that what you will.
"Also some antivirus programs can trip up Cygwin"
That could well be a contributing factor in my case.
Windows lacks fork(), or at least it's not documented. To implement the Cygwin folks have to go through a lot of tricks to implement it. And one of them is rebasing all dlls to start at different addresses.
There is a tool to rebase everything, and it's usually started after install. It's possible that after you have recompiled your own apps/dlls they might need rebasing too (speaking as a cygwin user, not developer).
The only thing that I found annoying in cygwin, is that I can't use all commands from the cmd.exe, because they make sense only under cygwin. For example "gcc" is just a cygwin symbolic link to "gcc-something.exe", and when you "run it" it gives "Access denied". The workaround is to run like this: sh -c "gcc <args>" from cmd.exe
But it might solve very hard problems, for example - redis (from antirez's depot) compiled with cygwin worked for me, and although there is much better windows version by the MSOpenTech guys, it just shows that sometimes it might be the only reasonable way. The other app that comes in mind is rsync.
> Windows lacks fork(), or at least it's not documented.
The NT kernel supports forking, but the Win32 subsystem does not. Because Interix lives outside the Win32 subsystem, it can provide a proper fork() implementation, whereas Cygwin has to live with its somewhat brittle emulation.
As I understand it, the problem lies with making the different subsystems interact: Forking itself is reasonably easy using NtCreateProcess(), but the Win32 subsystem won't know how to deal with the forked process and stuff will break, including console output.
I don't see Microsoft adding forking support to the Win32 subsystem any time soon, so you'd end up rewriting Cygwin from scratch by reverse engineering Interix...
The biggest problem - and what I suspect is happening to you - is when you have third-party programs and utilities that interfere with Cygwin, most often by putting an older or newer version of cygwin1.dll on the $PATH (i.e. you may be using Cygwin as part of some other program and not be aware of it). Cygwin uses shared memory; multiple versions of cygwin1.dll disagree on the format of this shared memory, and things go pear-shaped pretty quickly from there.
Also some antivirus programs can trip up Cygwin; in its emulation, it sometimes has cause to open, close then open files in quick succession, but AV programs sometimes analyse files when they are opened by programs, and cause bogus timing-dependent sharing errors.