Well if it worked fine before, clearly the problem doesn't lie with Switch. There could be possibly something strange going in with the specific files, but it's hard to say. Any chance you could send a sample file that doesn't work to me at tj[at]nch.com.au ? Otherwise it is difficult to help you any further....
Are all the files m4a files, or are some m4p files? m4p is a copy protected format and doesn't work with our software.