>>Not sure what you mean by that - can you elaborate?
>
>Each server has its IIS installed locally. Their root Web site is located however on the NAS. But, as any ASP.NET application, whenever an .aspx page is accessed for the first time, it will read it from the disk and cache it. The first hit to every .aspx page is a little bit longer. That comes after the DLL have been compiled into the IIS architecture. But, after that, if all there is is database requests returning HTML content, then there isn't much a NAS usage required.
>
>>It's worth pointing out that default Samba/SMB settings even on some high-end well-regarded NASs are not always compatible with all Windows functions e.g. http://forum.qnap.com/viewtopic.php?f=189&t=48793
>
>Ok, that is scary. Let me verfy what is the NAS we have.

UPDATE:

It's worth pointing out that default Samba/SMB settings even on some high-end well-regarded NASs are not always compatible with all Windows functions e.g. http://forum.qnap.com/viewtopic.php?f=189&t=48793 . However, in your particular case I'd expect an SMB misconfiguration to result in an operation failure rather than a long delay but eventual success.

I like Gregory's idea about checking power saving states. For the NAS that would be disks/network connections/overall device. You may also need to check the Windows server; it may connect to the NAS via a different NIC and that NIC may be set to power-save. Some so-called "green" switches or routers may also power down "inactive" ports.

In my experience I have never seen a case where power saving in a server environment is worthwhile. All it takes is one foulup caused by an inappropriate or too-aggressive power saving setting and the time it takes to troubleshoot it costs more than all the power that might be saved over the lifespan of the device.

I imagine power saving settings are useful and reliable with enterprise-grade equipment in large datacenter environments but that's not my line of business. For small/medium business usually the best bet is to go through the settings in detail and completely disable all power saving features.