From what I've read, it looks like the problem is related to neither Microsoft's operating system nor Linux, but is instead a consequence of extremely poor IT management and design. A poor workman blames his tools.
You can build rock-solid systems on either type of operating system. You can also build garbage on either OS. If the previous system was using C# or .NET, those are already bad signs. A switch to Linux is also a bad sign. Both actions imply that the end user was simply trying to find the absolute cheapest, quickest "solution," without any regard for testing, safety, reliability, recovery, performance, etc.
You get what you pay for, and if you don't know how to write specs and/or don't know anything about IT, you usually get even less than you pay for.