So your problem has nothing to do with Greek hyphenation, it’s about the way 
you define your \CritApp command. You could have shown the same problem with an 
English text. It appears that injecting the word via your macro breaks 
hyphenation, but I assume Hans and Wolfgang  will know better about that. 
Example without Greek:

\showframe
\mainlanguage[en]
\setuplanguage[en][patterns={en, agr}]
\definepapersize[HippPaper][width=6in, height=9in]
\setuppapersize[HippPaper]

\definefontfamily[mainface][serif][FreeSerif]
\setupbodyfont[mainface, 13pt]

\unexpanded\def\doCritApp#1#2#3%
  {\startlinenote[#1]{#2 #3}#2\stoplinenote[#1]}

\newcounter\MyCounter
\unexpanded\def\CritApp
  {\doglobal\increment\MyCounter
   \normalexpanded{\doCritApp{Varia:\MyCounter}}}

\starttext
supercalifragilisticexpialidocious
\CritApp{supercalifragilisticexpialidocious}{test}
\stoptext


On 18 Sep 2014, at 08:33, Pablo Rodriguez <oi...@gmx.es> wrote:

> Many thanks for the reply, Thomas.
> 
> My sample is the following:
> 
> \showframe
> \mainlanguage[en]
> \setuplanguage[en][patterns={en, agr}]
> \definepapersize[HippPaper][width=6in, height=9in]
> \setuppapersize[HippPaper]
> 
> \definefontfamily[mainface][serif][FreeSerif]
> \setupbodyfont[mainface, 13pt]
> 
> \unexpanded\def\doCritApp#1#2#3%
>   {\startlinenote[#1]{#2 #3}#2\stoplinenote[#1]}
> 
> \newcounter\MyCounter
> \unexpanded\def\CritApp
>   {\doglobal\increment\MyCounter
>    \normalexpanded{\doCritApp{Varia:\MyCounter}}}
> 
> %~ \def\CritApp#1#2{#1}
> 
> \starttext
> με τὴν τέχνην ταύτην \CritApp{ἴσα}{neut. pl. acc. adverbial, “equally
> to” + dat.} γενέτῃσιν ἐμοῖς, καὶ βίου \CritApp{κοινώσεσθαι}{fut. inf.
> with ὄμνυμι “to be a partner of” + gen.}
> \stoptext
> 
> After reading again the message that gave me the macro, hyphenation
> seems to be an unsolved issue with that command.
> 
> Many tganks for your help,

--
Prof. Dr. Thomas A. Schmitz
Geschäftsführender Direktor
Institut für Klassische und Romanische Philologie
Universität Bonn
Am Hof 1e
53113 Bonn
http://www.philologie.uni-bonn.de/personal/schmitz

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