There is a problem with the way current calibre versions store the comments and the way the Kobo devices parse them. It is a known problem and has been discussed a couple of times. See
Kobo Aura HD: Extra paragraph breaks in Synopsis. for an explanation and a workaround.
But, if you are stripping the HTML tags out, then it will be only how the device is handling the line breaks. How are you doing that? If you edit the comments in calibre through the metadata editor, it will always save it as HTML, not plain text.