Comix currently takes the next archive in the working directory without 'smart' sorting the files first, which can lead to sudden jumps in volumes/chapters/issues while reading continuously.
I.e. a directory contains '1.cbz', '2.cbz', <etc>, '10.cbz'.
Comix currently jumps from 1.cbz to 10.cbz and then to 2.cbz.
Haven't tested how Comix handles case sensitivity, but might also be worth looking into.
Many file organizers sadly don't bother with zero fill and many modern file browsers seem to evaluate the full filename before sorting.