I would have hoped you would have made backups of your files before overwriting them, just so you can compare the original files with the converted files and check things like quality, filesize etc. There is unfortunately nothing we can do in this scenario sorry.
I am happy to send you the latest (soon to be released) Switch and see if you have better luck with what you are trying to do. If you would like me to do that, send me an email at tj [at] nch.com.au and let me know.