I recently made use of the html viewer code in the AnnotationViewerDialog class, using the html viewer alternative. It uses as input a version of the CAS produced by CasToInlineXml (line 445). If the annotations involved are nested, the result has extra line feeds and lots of extra white space (corresponding to the indenting of the nested xml elements produced by the CasToInlineXml).
The fix is (now) easy since we've recently added a flag to control the indenting. Change this (and other uses as appropriate) to set the (new) formattedOutput flag of CasToInlineXml to false.