Hello Stephen,
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The problem with the 2 sites was that a rouge SQL Server connection was causing SQL Server to hog the cpu thereby not allowing my sites to load.
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Yes, Keane restarted SQL service as several threads of this process found running and hence overloading the CPU. To avoid any more issues he restarted the service which took max 3 - 4 minutes.
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The user name/password dialog was caused by security rights issues.
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Whenever you create any web site from Plesk control panel, Plesk assign default permissions to it but some web sites need special permissions like Write/Modify which we can assign it manually on server. In case if you make any changes with domain from "Setup" section of Plesk, Plesk execute one of its utility called websrvmng.exe to recalculate the permissions and remove these permissions considering as security risk. In this case site starts prompting for login box as websrvmng.exe have removed permissions of IUSR. We reassign permissions to IUSR to fix this issue.
The permissions get reset when any of the following happen from Plesk -
1] You reset password of main FTP user/additional user.
2] You edit main FTP user name/additional user name from Setup.
3] Enable/Disable FP extensions.
4] Change version of PHP or ASP .NET.
5] Enable/disable additional script languages from Setup.
6] Add/remove Dedicated Application Pool.
We have found a fix for this permission reset issue so that in future it will not reset permissions of your web site even if you make any changes with it from Plesk.
We have setup a new Windows shared server. If you want we can migrate your account on this server.