I have a fix for this though I have been unable to post it to gemini, it may be a bit of a hack but as far as I can see the wiki module processes the line breaks again in WWWikiDB.vd line 761 - 767.
To fix this I have commented out lines 762- 765 so that the in put is not processed at all.

Protected Function ProcessLineBreaks(ByVal val As String) As String
  'val.Replace("\b\r\n", "<br>")
  '//val = Regex.Replace(val, "([^\>])\r\n", "$1<br>", C_C_Options) ' ...not prefixed with a > (because we don't want to add it after most HTML closing tags)
  'val = Regex.Replace(val, "([biua]\>)\r\n", "$1<br>", C_C_Options) ' ...prefixed by b> i> u> a> (because we do want it after these HTML tags)
  'val = Regex.Replace(val, "\<br\>\r\n", "<br><br>", C_C_Options) ' ...prefixed by <br> (and this other one)
  Return val
End Function

Due to another bug that I needed fixed also I have packaged this up into another source package available from http://ewds.strath.ac.uk/Development.aspx I hope someone finds this of use.