I found the answer, so I’m posting it to help others out:
In this file (depending on your server setup):
/etc/php5/apache2/conf.d
Change suhosin.ini on the following lines (remove the semicolons if applicable):
suhosin.post.max_vars = 5000
suhosin.request.max_vars = 5000
The default 1000 will not work – 5000 seems to work well for my needs (so far!)
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