The original AtomicParsley.exe version I had is 412 KB, the new one is 457 KB, they are definitely not the same. I'm not sure beyond that how to tell what the difference is, but they can't be the same.
In any case, I reverted to the old version and I managed to get the error again. When it happens, a modal dialog appears with:
AtomicParsley.exe has stopped working
A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available.
After that it hangs on the modal window. I believe conversion has actually succeeded in spite of the error, and the resulting file is playable.
I've uploaded the contents of the output area to: http://pastebin.com/hhHP55UJ
. (I had to skip some of the middle to get under 500K limit, but the beginning and end are there.) I also still have the debug log, the original .wtv file (6.5G), and the converted files, if those would help.