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.

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.