Is there 2 popups built into windows2000 I keep getting 1 popup 4"x4"gray that says Messenger Service
in the left hand corner.

Message from System to Alert on current date and time.

Microsoft Windows has encounted an Internal Error
Your windows registry is corrpted.
Microsoft recommends a complete system scan.

Microsoft recommends

http://www.msreg.com

To repair for a free download

It popsup about every 10minutes

There another bigger one that does the same thing.

Anyone know how to stop them?

That is messenger spam.

The same type of miscreants who screw up your computer with popups and other malware have figured out how to use Messenger Service (not to be confused with AOL IM or MSN IM or ICQ or whatever) to spam you.

This Messenger Service was created for network administrators to message computers on their lans. You do not need it running.

The best thing to do is to shut it off.

Messenger (not to be confused with MSN Messenger, AOL IM or any other internet messenger) was originally created for system administrators and users to communicate with other users on large networks.
Spammers have figured out how to send spam with it taking advantage of exploits on your computer.
What you describes sounds like
Windows Messenger Spam
To block the spam is to turn off Messenger Service.
To do that:
--In Windows XP, click Start>>Control Panel
--In Windows 2000, click Start>>Settings>>Control Panel
In both versions:
--Double click Administrative Tools
--Double click Services
--Double click Messenger
--Under Service Status, click Stop
--In the box next to Startup Type, select Disabled
--Click Apply>>OK

Alternatively, you can download a small program that will disable Messenger Service called “Shoot The Messenger” which is available at
http://www.grc.com/freepopular.htm
Download and run “Shoot The Messenger”, which will disable Messenger Service.