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I have published an ArcGIS service based on a MXD I have generated the cached tiles on a shared NAS. When I access the Map Service with the build in js admin viewer (http://SERVER/arcgis/rest/service/....)

The map display quickly but, every now and then no tiles are coming for maybe 5 seconds, and then they all come quickly.

Why could that be? Any tip / ideas welcome? How to diagnose the problem?

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On your web server, create a script that wakes your services up every 15 minutes or so. Below is an example of a vbs file that the Windows Task Manager runs every 15 minutes:

'declare web app variable, set variable to be an IE application  
Dim webApp  
Set webApp= CreateObject("InternetExplorer.Application")  

'set visibility of the web app, can be set to false to run in the background  
webApp.Visible = true  

'declare a counter variable as integer, set it to zero  
Dim counter  
counter = 0  

'declare array to hold names of different services  
'simply increase the array by +1 and add a new entry for every new service that gets published  

dim services(6)   
services(0)="MapCache1/MapServer"  
services(1)="MapCache2/MapServer"  
services(2)="MapCache3/MapServer"  
services(3)="MapCache4/MapServer"  
services(4)="CompositeLocator/GeocodeServer"  
services(5)="Geometry/GeometryServer"  

dim map(4)  
map(0)="MapCache1/MapServer"  
map(1)="MapCache2/MapServer"  
map(2)="MapCache3/MapServer"  
map(3)="MapCache4/MapServer"  

'the following loop uses the REST API and the array to step through each service page  

Do while counter < 4  

    For Each x in services      
      webApp.Navigate "http://gisweb/ArcGIS/rest/services/"& x  
      wscript.sleep(2000)  
    Next

    For Each y in map  
      webApp.Navigate "http://gisweb/ArcGIS/rest/services/"& y & "?f=jsapi"  
      wscript.sleep(7000)  
    Next  

  counter = counter + 1  
Loop  

webApp.quit  
Set webApp = nothing  
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Assuming that you are using ArcGIS 10, try to clear your server cache here, if it makes problem.

and read this document Map caching tips and best practices with ArcGIS Server 10 here, if you have missed anything when making ceched map....

clearcache

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