After long hours of useless research I end up with removing php5 and php from Cygwin and mapping there standalone PHP for Windows.
For anyone facing this problem:
- Uninstall all "PHP" group of extensions for cygwin
- Run cygwin
rm -f /usr/bin/php.exe
rm -rf /usr/share/php
- Download and install brand new PHP for Windows
ln -s /cygdrive/c/your/path/to/php/php.exe /usr/bin/php.exe
So I don't know why this issue occured to me, but fresh native php for windows installation helped.