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"Your Maximum registry size is too small" Error won't go away

This is a problem I have been on and off struggling with to get rid of on a client's Windows 2000 server.  On startup they get the "Your Maximum registry size is too small" error.  I have tried changing the maximum value of registry size through System Properties.  I have also tried editing it through the registry (both of these attempts were from EExchange questions).  I even tried doing some spyware/virus scans but the server does not appear compromised.

I have somewhat given up on this but the client keeps asking about it.  Is there anything else I can look at that might find the root of this problem?
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tboy6423
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There are  2 other things you can do, you can use a registry cleaner or override the warning:
http://utools.com/help/DlgOverride.asp 
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I have tried RegistryMechanic, RegClean, and Tweaknow RegCleaner.  On top of that I have attempted to walk through the "override" idea as well but to no avail.  I do not get any opportunity to Override.  That article mentions that not all errors can be overridden, perhaps this is an example.

Out of ideas, again. :-\
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This being a server, isn't there inherent risk associated with a Windows Repair?

This isn't a Huge issue to the client, just an annoyance, if there is any risk we can live with the error as we have been.
There is a possilbility with some program files going missing:
http://www.windowsnetworking.com/kbase/WindowsTips/Windows2000/AdminTips/TroubleShooting/ManualvsFastRepairinWindows2000.html
The only other thing i can suggest is doing a registry scan, here are some free ones, it might be able to fix the issue:
http://www.pcworld.com/downloads/file/fid,64953-order,1-page,1-c,systemresourcestuneup/description.html 
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I have already performed numerous registry scans to no avail.  Also, I don't think a repair is an option, as this is a vital server.

I suppose if those are the only options it looks like we can't resolve this.
What did you change the maximum value to? What was it before?
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I changed the maximum registry size to many different values.  Current Registry Size reports 89 MB, which seems massive.

I have tried 100, 200, 400, and it's currently set at 0.  All of those settings still yield the error.
Is it a windows 2000 Advanced server?
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I'm not sure how to tell if it's the Advanced version or not, but System Properties reports Windows 2000 5.00.2195 SP4
go to start , run, then type, winver What does it say?
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Microsoft Windows 2000 Version 5.0 (Build 2195: Service Pack 4)
This may sound silly, but change the Maxium size to 93MB and reboot, let me know if the error still come up
I did happen to find a KB regarding this, it may fix your error...
http://support.microsoft.com/kb/906952
You may want to try this one first....http://support.microsoft.com/kb/312362
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We were not able to repair the server but it would've fixed the issue most likely.