First things first, thank you all for contributions of help and support.

Second thing, this physical server has run Windows Server 2003 R2 Standard (64-bit) for 2 years without any issues. This is not a hardware issue.

Hardware specs:

• 2x Opteron 845 Dual-Core (4 physical cores at 2.0GHz)
• 12GB DDR ECC/R 266MHz
• 250GB SATA-II System Hard Drive
• 2TB SATA-II RAID Storage Array

OS: Windows Server 2008 Enterprise (64-bit)

Roles:

• Active Directory Domain Services
• Application Server
• DHCP Server
• DNS Server
• File Services
• Network Policy and Access Services
• Web Server (IIS)

Features:

• .NET Framework 3.0
• Group Policy Management
• Remote Server Administration Tools
• Windows Internal Database
• Windows Process Activation Service

Symptoms:

• After 64-96 hours of uptime, entire operations lag heavily. See below for list.
• Browsing server shares from the network; remotely logging onto the server via Remote Desktop; logging onto any workstation joined to the domain; logging off any workstation joined to the domain.
• "Lag" is defined as: the workstation/server sits for 3-10 minutes with 0% CPU usage after initiating the command. Explorer.exe is always unresponsive during this time.
• When I restart the ADDC (Server 2008) the symptoms dissappear for at least 36 hours.
• IIS, FTP, and VPN services are unaffected.

I have attempted to disabled completely the IPv6 service on all the workstations and the ADDC. This has no effect. I was also running VMware Server 2.0 (Final) on the Server 2008 machine and uninstalling this service has no effect on the issue. This server build is about 3 months old, and unfortunately I cannot correlate the issue appearing after any specific action. I am very hesitant to dump everything and reload the system with a new domain as I have everything configured as I want. I do not have much free time to do such a thing. When the server works fine, everything is configured perfectly. Sometimes I can cause a preemptive strike by restarting the server every night, but that should not be how a server is operated. I am very frustrated by the issue and so are the users. Performance is excellent when everything operates normally. Even with four Virtual Machines, everything was great.

Again, any help is appreciated. I have scoured Google, spoken with other skilled Microsoft professionals, and done all the troubleshooting I can think of. Nothing seems to affect the issue.

Thanks in advance.
A.J.

Server 2008 and Vista have some great performance monitoring tools. They will help you track down the issue.

Helpful...

...but not.

Anything more to suggest? I don't even know what I'm looking for.

Did you try it?

Sure did.

No idea what I'm looking for while it's lagging, though. The processors are at idle, network utilization is idle, disk throughput is idle, memory access is idle.

here is great way to create some logs and figure out what is going,

http://www.petri.co.il/analyze-windows-performance-logs.htm

If restarting the ADDC on the 2008 box resolves the issues for a time, it would appear that it's likely there is a resource leak in the ADDC service process - could be memory, could be a blocking queue growth, etc. Performance Monitor, tasking against this specific process, might be your best place to start. Also, include the memory counters for all processes on the system (not _TOTAL, but all individual processes):

Under the "Process" object, selecting :<All instances>", add:
- Handle Count
- Pool Nonpaged Bytes
- Pool Paged Bytes
- Private Bytes
- Virtual Bytes
- Working Set
- Working Set - Private

Hi,

If this seems to be related to network issues / performance on networking, then I have had the following problem (even though it is a mixture of OS and HW / drivers). On many of our servers which were working greate with 2003 (as u mention) we saw a decrease in performance over network performance once we got 2008 up and running (x64 Enteprise as well). Finally, it was resolved by disabling SNP (Scalable Network Package) that is default enabled from 2003 SP2 and forward. SNP can be disabled trough the registry or in some case turned of from BIOS (most often TOE) or the driver package that u r running.

Otherwise, my history tells me, when really wiered stuff is happening, check the drivers and try updating them.... needle in a haystack but anyway

Might be it.... u never know.

I was kind of having the same problems untill I manually changed the DNS server settings on the client pc'c to point to the DNS Server.

Do what Cluberti said, as this gets worse over time monitoring is the only way you are going to find any trends / patterns in resource usage and allocation.

266MHz RAM? Is that normal for a Server 2008 capable platform!?!?

Hmm also something about what you said before... not being a hardware issue. Said you ran 2003 on this for 2 years. I am asking this now, is all of your hardware 2008 certified?

Hmm,
"this physical server has run Windows Server 2003 R2 Standard (64-bit) for 2 years without any issues. This is not a hardware issue."
"This server build is about 3 months old, and unfortunately I cannot correlate the issue appearing after any specific action."
witch is it? If it's several years old I find it hard to belive it's 2008 ready, if it's not several years old I'd go with the suggestion from fizban2