I have not read about an instal pop-up window before. I do know that when a reinstal is incomplete/interrupted (after windows 2000 setup has copied temporary installation files to the hard disk), you will get a "dual boot" option screen when you start the computer, giving you the choice of "Microsoft Windows 2000 Professional Setup" as the default, and "Microsoft Windows 2000 Professional" (which is your normal OS) as the 2nd option.
If it applies to your case, read on.
To get rid of that (and the temporary installation files), you need to (1) edit the C:\boot.ini file; and (2) delete the temporary installation folder copied to your hard disk.
To edit boot.ini, right click My Computer icon, Properties, Advanced tab, select Startup and Recovery. For the default operating system, click the drop down list and select "Microsoft Windows 2000 Professional" /fastdetect as the default. Click OK, OK.
Then use My Computer or Explorer to go to your local disk C drive. Click Tools on the menu, select Folder Options, View tab. Tick "Show all hidden files and folders", untick "Hide all known file extensions", and untick "Hide protected operating system files". Click OK.
You should now see the file boot.ini under the C drive.
Right click boot.ini and select "opens with". Then select Notepad. Boot.ini will open in Notepad.
Now delete one of the lines under [operating systems] that reads C:\$WIN_NT$.~BT\BOOTSECT.DAT="Microsoft Windows 2000 Professional Setup"
This ought to be the first line under [operating systems].
Just to make sure, your boot.ini file should now read:
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
This assumes that your C partition is on the 1st partition, on your first IDE hard disk (which is usually the case).
Save the changes and exit Notepad.
Restart the computer. You should boot straight into Windows 2000 proper without getting the dual boot screen.
Once in Windows 2000, go to your C drive again and delete the entire folder called $WIN_NT$.~BT which is the temporary folder where installation files are stored, and would have been removed by Windows 2000 Setup had you completed the reinstallation.
If the above does not apply to you, post back with details of what the "popup window' says.