I have to problems.

If you look at http://www.sermonspeaker.net/download/language-packs.html you see that some languages are listed twice. Like English, German, Russian and Chinese. I had this happen for some time now and my guess is that if someone translates multiple files on Transifex in a short time, like when updating only a few strings in multiple files, then the webhooks fires to fast and cTransifex gets confused. But that's just a guess :-)

Usually I was able to just recreate the files using the "Get Data" button in the backend. But when I tried to do that today the button did nothing. In fact the whole modal goes through the roof (only partially visible on top) when opening. It comes back to normal when I resize the browser to a smaller width. But clicking the "Get Data" button seems to do nothing at all.
Tested using IE11 and Chrome on Joomla 3.1.5.
Using the developer tools I see that the button requests the link "administrator/index.php?option=com_ctransifex&task=transifex.resources&format=raw" and stays at "pending".

Edit: Just saw in error logs:
[Tue Sep 24 19:43:10 2013] [warn] [client http://www.xxx.yyy.zzz] Timeout waiting for output from CGI script /path/to/php, referer: http://www.example.com/administrator/index.php?option=com_ctransifex&view=projects#
[Tue Sep 24 19:43:10 2013] [error] [client http://www.xxx.yyy.zzz] Script timed out before returning headers: php, referer: http://www.example.com/administrator/index.php?option=com_ctransifex&view=projects#