I was having the same problem with /usr/bin/net getting hung up and not closing. I have zabbix installed to monitor the server, and after a few days, the memory started getting full. I started to notice this after installing btsync to sync some shares with windows computers.
Anyway, I thought about commenting out the cron.d line. But I figure they added it for some reason (would be nice if someone from zentyal let us know why....). So I decided to change the line to this:
nano /etc/cron.d/zentyal-samba
* * * * * root /usr/bin/timeout 50s /usr/bin/net cache flush > /dev/null
The timeout command will only allow the net command to run for a maximum of 50 seconds. It seems to be working for me so far.
Note: Timeout was already installed on my machine, however, you probably want to make sure it's installed on yours first. Also, any future zentyal upgrade will probably overwrite the change...