Network shares disappear from desktop

Hi,
I have searched but cannot find a thread which outlines the problem I am having.
I have a 40 strong iMac network with 2 Mac Mini servers. All iMacs are running Mountain Lion (10.8.2) with the Mac Mini's running Mountain Lion (10.8.2) and Server (2.1.1). I have a number of network shares defined which are hosted on a Pegasus array connected via a thunderbolt cable to one of the Mac Mini's. The shares mount as part of the login profile for each user.
The problem I am having is that the desktop icons for the shares randomly disapear from the desktop. This typically happens to 2, 3, or 4 of the shares but never all of them at once. When I go into the Connect to Server option in Finder and connect to the server hosting the shares they appear as available for connection (i.e. they are not greyed out as if an existing connection exists with the share).
As a general rule, the end users leave their machines on overnight and don't usually shut them down.
Can anyone shed any light as to why these shares seem to be randomly disconnecting / ejecting?
Cheers,
Tzukius.

Kevin,
All shares are done via AFP. When I look at the stats on the CPU on the server app it is hovering around 3-5% for a 4hr average.
One thing I have noticed is that on my machine I never lose the connections, co-incedentaly, my machine never enters sleep mode whereas the other machines are set to sleep after 30mins. I'm starting to think that this may be the cause of my problem, even though the ethernet interface is used for connecting the machines to the network and not the wireless connection (I had read on a couple of other threads that this can cause the disconnection of network shares).

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We need to know some basic scoping information to provide any further input.
1)
Is the user prompted that the server will be shutting down?
2)
Does Task Scheduler show that the task ran at the scheduled time?
3)
Are there any errors in %windir%\tasks\schedlgu.txt?
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Steps to clean boot machine:
================
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Network shares disappear from desktop

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