We have a MacMini 16 GB / 500 HD + 120 SSD acting as a FM server for 12 local machines, 6 remote and 20 ipads, the fact is that from time to time the server stops responding smoothly as ever an starts dropping connections, ping into another machine decrease the problem but still remains.

We suspect first at the beginning of a network problem, but if we ping the FMServer and a printer from a 3rd machine, the packets going to the FMS drops frecuently (20-40% loss) and the packets to the printer are 100% clean.

The FMS its a fresh installed 10.9.2 updated to 10.9.5 no server no FileSharing, no remote session, Spotlight disabled, running at 1% acording to TOP and activity monitor only Remote desktop.

Any advice what to look into ?

I'm no expert on this, but it might be a simple case of a Mac mini not being up to the task of serving potentially 38 clients at once. The packet loss, however, does point to a network issue.

I have the java automatic updates disabled (as recommended) but I have noticed that Java announces (without installing) the java update via a dialog box (v 67 -> 71 in this case) after installing the update, repaired permissions and restarted, the network (ping) problems have gone (now 100% perfect) and the ipads are able to sync without a problem and the remote users are no longer loosing the connection every four to five minutes, I noticed that dialog box 20 mins before leaving so, we will have to wait until tomorrow to know for sure.

Its possible that the Java dialog box announcing the update generate all this mess even if if the update its not installed ?