Windows 2000 Server runs all services but no applications

I have a Dell PowerEdge Server 1550 with Windows 2000 Server installed. This weekend I decided to reboot the server since it had not been rebooted in quite a while and after rebooting I found out all services loaded but no applications will run. Here's a detailed description:

The server starts up, Windows 2000 Server loads, asks for Administrator password, and after logging in nothing happens (explorer.exe doesn't load so no desktop, no icons and no task bar are available). I open up the Task Manager and find all services loaded (there's e-mail, web services, etc, everything works fine) but no explorer.exe... I try tu run it manually but it only shows up in the process list for a fraction of a second and then disappears. I try tu run "cmd" but the same happens. Any application I try to run does exactly the same (appears in the list for a fraction of a second and then closes).

Rebooting in safe mode presents exactly the same scenario. I tried rebooting in safe mode with command prompt (which worked) and tried to run "sfc /scannow" but it says the RPC server is unavailable. I tried booting from the Windows 2000 Server CD and from the Repair Console ran "chkdsk /r", it ran for a while and then said one or more errors were found and repaired. I rebooted but everything's still the same.

I'm stumped, any ideas? This is a mission critical server so I can't take it offline too much time. The only good thing is that all services are running fine including Exchange, IIS, Lotus Domino, etc.
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Pete LongTechnical ConsultantCommented:
How to Perform an In-Place Upgrade of Windows 2000;en-us;292175

Repairing, Recovering, and Restoring an Installation of Windows 2000;en-us;268106

Differences Between Manual and Fast Repair in Windows;en-us;238359

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gabolincheAuthor Commented:
Ok, I'm willing to try a Fast Repair on the server but the KB article says "If you do these options on a Windows 2000 Server domain controller you run the risk of overwriting the Active directory database"... After backing up the Active Directory database (which I don't know if I will be able to do with the limited access I have to the server), is there anything else I should back up? This is a domain controller running all services including IIS, Exchange, DNS, etc...
Pete LongTechnical ConsultantCommented:
is it the only domain controller you have?
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gabolincheAuthor Commented:
Yes, it is the only domain controller...
gabolincheAuthor Commented:
Actually I also have doubts about how to backup the Active Directory database. Everywhere I search I find how to do it with the Backup utility that comes with Windows 2000 but I have no access to that utility right now. Is it enough to just copy the files ntds.dit , edb.chk , edb.log , res1.log and res2.log found in the SystemRoot\NTDS folder?
Pete LongTechnical ConsultantCommented:
can you promote something else while the server is up (or appears to be up?)
gabolincheAuthor Commented:
Mmhh... probably not, I have no other computer with Windows 2000 Server installed...
Pete LongTechnical ConsultantCommented:
Well If I were you Id get a decent PC, install server 2000 on it, install DNS on it,

click start > run > dcpromo

to promote it to domain controller

then SEIZE all the FSMO roles from the dodgy server

To seize or transfer the FSMO roles by using Ntdsutil, follow these steps:
1.      On any domain controller, click Start, click Run, type ntdsutil in the Open box, and then click OK.

Note Microsoft recommends that you use the domain controller that is taking the FSMO roles.
2.      Type roles, and then press ENTER.

To see a list of available commands at any of the prompts in the Ntdsutil tool, type ?, and then press ENTER.
3.      Type connections, and then press ENTER.
4.      Type connect to server servername, where servername is the name of the server you want to use, and then press ENTER.
5.      At the server connections: prompt, type q, and then press ENTER again.
6.      Type seize role, where role is the role you want to seize. For a list of roles that you can seize, type ? at the Fsmo maintenance: prompt, and then press ENTER, or consult the list of roles at the beginning of this article. For example, to seize the RID Master role, you would type seize rid master. The one exception is for the PDC Emulator role, whose syntax would be "seize pdc" and not "seize pdc emulator".

Note All five roles need to be in the forest. If the first domain controller is out of the forest then seize all roles. Determine which roles are to be on which remaining domain controllers so that all five roles are not on only one server.

Microsoft recommends that you only seize all roles when the other domain controller is not returning to the domain, otherwise fix the broken domain controller with the roles.

If the original domain controller with the FSMO roles is still online, transfer the roles. Type transfer role.
7.      After you seize or transfer the roles, type q, and then press ENTER until you quit the Ntdsutil tool.
Note Do not put the Infrastructure Master role on the same domain controller as the global catalogue.;EN-US;197132

To check if a domain controller is also a global catalogue server:
1.      Click Start, point to Programs, point to Administrative Tools, and then click Active Directory Sites and Services.
2.      Double-click Sites in the left pane, and then browse to the appropriate site or click Default-first-site-name if no other sites are available.
3.      Open the Servers folder, and then click the domain controller.
4.      In the domain controller's folder, double-click NTDS Settings.
5.      On the Action menu, click Properties.
6.      On the General tab, locate the Global Catalogue check box to see if it is selected.

Using Ntdsutil.exe to Seize or Transfer FSMO Roles to a Domain Controller

Windows 2000 Active Directory FSMO Roles;EN-US;197132

Flexible Single Master Operation Transfer and Seizure Process;EN-US;223787
gabolincheAuthor Commented:
Thanks Pete, I'll give it a shot and comment back when done...
Pete LongTechnical ConsultantCommented:
no problem that way you get to keep a LIVE copy of Active directory and things can stay online (if your clients are staying online remember the DNS IP has changed)
gabolincheAuthor Commented:
Well, what happened and what caused this situation still remains a mistery... I had to perform an in-place upgrade and apparently everything returned back to normal. Nothing was lost (even the Active Directory prevailed) except for a couple of registry entries that messed up the Exchange System Attendant but I just replaced them and everything worked fine.
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