Since you are having the same problem across different programs, have you considered hardware as the source of the errors? Video encoding tends to push your computer harder than many other tasks, so you may be overheating the cpu. Check the heatsink/fan on the cpu to make sure it isn't clogged up with dust.
I'd also check the memory for errors. Run Memtest86 for a few hours. If you see any errors from it, you'll need to replace the ram (though you might be able to adjust the voltage and get it stable).