Since yesterday's (22.6.2015) update, my MiKTeX 2.9 on Windows 8.1 64-bit repeatedly crashes with an error message that is something like:
This file is not present either in the MiKTeX binaries folder or in my system.
The error is due to the on-the-fly installation of missing packages. When the "ask me first" is used miktex tries to show a dialog and fails. This explains the erratic number of documents showing the problem.
I made a bug report. In the meantime one can avoid the crash by setting the option to "yes" or "no", and by installing missing package before the compilation.