This won't be much help, but we've definitely had occasional issues where Sorenson claims it's successfully encoded a clip (WMV) and then, when you go to play it, the clip is corrupt and unreadable. It only seems to happen when I batch a large number of files to encode, so I don't know if it's related to that, but when we have it watch a folder instead of batching the files, we don't seem to have that problem.

Also, while I haven't used 4.3, 4.2 did erratic things and was pretty much unusable on a computer with an Athlon 64, but works fine on an Intel machine.