If you have : in favorites folder name, then it will put new bookmark in the wrong newly created folder no matter what. Perhaps the root of the problem is in "C:" and not just ":", but i haven't tested this and just noticed this weird behavior...
For example i have bookmark folders:
rare (C: W:)
So, when i try to add new bookmark into "SOMENAME" folder DOpus instead will create new "rare (C:" folder at the top of the bookmarks tree and then it will create "SOMENAME" and then put my new bookmarks here.
So the final destination will be
rare (C: > SOMENAME > NEWBOOKMARKS
SOMENAME > NEWBOOKMARKS