By default Pure-ftpd limits you to only being able to list < 2000 files.
To change this, do the following..
Edit your pure-ftpd config file – usually in /etc/pure-ftpd.conf
change the line
LimitRecursion 2000 8
LimitRecursion xxxx 8
Where xxxx is the number of files you want to limit it to…
Restart the pure-ftpd service and you should be done!