It looks like the Latin characters are vertical (as they should be), but each character is flipped along the horizontal plane. I don't understand why that is happening.
Please try loading the attached public domain EPUB file of 阿Ｑ正傳 from Project Gutenberg on your Kobo and see what happens.
On the Kindle, the double-space Latin characters are vertical and the normal space Latin characters are tipped on their side. This is the correct presentation.
For the command line to recursively convert all EPUB files into vertical traditional, Taiwan EPUB file try the following command. It will walk down your file structure, convert every EPUB file, and save the converted file in the same location but with a "T" suffix (e.g. 阿Ｑ正傳.epub -> 阿Ｑ正傳T.epub). The original file is unchanged.
Code:
calibre-debug --run-plugin "Chinese Text Conversion" -- -ol tw -il cn -d s2t -qt e -td v -tdo r -a T **/*.epub
The first post in this thread has some usage instructions for the command line.