Today I had the same problem with creating the mailfilters due ispconfig3.
The mailfilter was not created automatically and the mailfilters directory was clean.
After some research, I have founded out that the maildrop plugin was not correct enabled. Maybe a problem on a update or install script? Im not sure, because i had to update after i have installed the system^^.
A simple softlink fixes the problem
ln -s /usr/local/ispconfig/server/plugins-available/maildrop_plugin.inc.php /usr/local/ispconfig/server/plugins-enabled/maildrop_plugin.inc.php
P.S.: I am using Courier with maildrop and currently ISPConfig 126.96.36.199