Open blank html file or create new file in Geany and set it type to html (not necessary to save the file). Type <script> and </script> (if autocompletion switched off).
Move cursor in the middle of the tag (beetween > and <), press enter twice. Second tag will loose its color.
Os: Debian Squeeze
Application: Geany 0.19
I already report this bug to Geany tracker, but developer says that it is Scintilla lexer problem...