I posted this question a few weeks back on the Phx forum and no one seems to have an answer.
http://modxcms.com/forums/index.php/topic,50627.0.html
Could it be an issue with how Phx works with YAMS? Additionally, if I replace ((yams_data:[+id+]:content_(yams_id))) with [+content_en+] in the chunk that does not work, the word_limit behaves properly again.