featured.py puts {{Link FA}} either before all interwikis or right next to the affected interwiki depending on the wiki setting. Nevertheless, interwiki.py always moves {{Link FA}} to the top of interwikis no matter what language is being updated.
There have been recent issues with the relocation of stub and {{Link FA}} templates using category.py. See http://en.wikipedia.org/w/index.php?title=Wikipedia:Administrators%27_noticeboard/Incidents&oldid=465991424#Reedy_Bot
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There have been recent issues with the relocation of stub and {{Link FA}} templates using category.py. See http://en.wikipedia.org/w/index.php?title=Wikipedia:Administrators%27_noticeboard/Incidents&oldid=465991424#Reedy_Bot