This could be almost any hardware problem, from overheating the CPU to a bad memory chip. If you have a 3rd-party capture card like Matrox or Aja installed, the odds go up if the drivers for those cards aren’t perfectly matched to your setup.
Software conflicts will usually result from codecs that get installed at the system level and interfere with Premiere/Encore when the video is transcoded. Look for other encoders or DVD players that you have installed, especially any “free” versions that you may have acquired.
Finding the cause (and fixing it!) will not be easy. At some point you may find it easier just to re-format and reinstall only Windows and your mission-critical apps. Unfortunately, if it’s a hardware problem, re-formatting and reinstalling won’t help at all.
-Jeff
The Focal Easy Guide to Adobe Encore DVD 2.0