IIRC, something resembling this happened to me when I
migrated from RH2000 to X5. I believe I was importing Word docs to
be used in the X5 built-in HTML editor. Of course, this was just
one of several formatting issues that process created.
Solution: Edit every topic and manually fix them all.
I had to audit and edit every topic due to other formatting
issues anyway, so I didn't think much of it. I can't remember which
ways I tried to import into X5 though (project import, CHM, and
each file separately I think, but that part of it is vague - it
happened nearly 2 years ago), so I can't say if one solves this
issue or not. All I know is that I spent about 2 hrs messing with
the import, didn't find a solution to my formatting problems (not
this problem specifically), and then decided to cut my losses and
start editing.
Due to this process, I have never been enamored with the
spell checker capabilities of RH's built-in HTML WYSIWYG editor -
many of these errors I only noticed after exporting to Word for a
printed manual.
Maybe someone else has had better luck.