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.