I've used this tool for a while now, but I find the new version (1.0.3.6) won't encode files properly. Here's the problem - I want to merge some files and not others on the same DVD

I add the first file, edit it and add other video streams I want to merge together. They are Mpeg2Video so in the new version I take advantage of 'copy meg2streams' to save time.
I go back to add more files to the main window to add other separate files. Having checked settings (why oh why is loop back set as a default??), I find after encoding, only the first merged file has been encoded, despite seeming to encode the others.

I have done this same process on a much older version of Flick and it works fine (though the version is so old I have to re-encode (is selecting 'copy mpeg2' option where I go wrong?)....or is it a bug in the new version maybe?