It's happened to a few DO-328s on approach too:
http://www.ntsb.gov/ntsb/brief.asp?ev_id=20020906X01547&key=1I don't know of any certified avionics systems that run on windows. Occasionally you have people doing a flight display running on a laptop, and those can be windows based but they are usually only personal projects. Just about all avionics out there are running on embedded systems. Many of the systems in years past have been quite bulky, heavy, and slow (by today's standards). Now, more and more off the shelf parts are becoming practical for use in avionics, though there is still a lot of customization necessary. Particularly, more standard processors are being used. Power PC has been a popular choice for some time, though other processors originally targeted for laptops are being used as well.
As for OS, many systems don't use any OS at all. If you don't need the advanced functionality of an OS (thread/process handling, filesystem, graphics, etc.) that there is not point in supporting all the overhead. Also, for certified avionics the testing requirements are extremely stringent and having an OS in the picture complicates that process even further. So if you don't need it, it's best not to have it. There are some applications where an operating system is preferable though. In most cases the choice will be linux. With linux, you have to ability to control precisely what the operating system includes and how it operates. This allows you to compact both the size of the operating system and to strip all functionality you don't need out of the kernal. It is not unfeasible to get an entire OS and file system down to under 16 MB.
That is not to say the windows is not or cannot be used in avionics and be completely stable. One of the main reasons instability creeps into programs is because there is such a diversity of hardware available for PCs that it is impossible to test for every case out there. Avionics do not have this issue as the hardware is known.
Anyway, there's sort of a scatter shot answer to your question. If you want to read more about avionics, the information is always available online:
http://en.wikipedia.org/wiki/Avionics