Hi Melody,
Sorry, I was also unable to reproduce the problem with Visual Studio till today, Currently I have a visual studio with default UI set that to match that of VSTA, like missing menu items for Watch 2, 3 & 4, build configuration default set to "Release" the UI for changing is also missing, but I can add these manually. See the screenshot.

This happened shortly after vsta.exe was run from the command prompt and it displayed a please wait while vsta confirm itself for first run. Which was not true.
When you mentioned the registry hive I think you must have meant it to be of "VSTAHostConfig"
I currently do have VS 2008 (SP1) , VS 2003 (SP1) and SQL Express 2008 (SP1) installed.
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\CombBuilder]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\CombBuilder\2.0]
"VSCSProjectTemplatesLocation"="D:\\Program Files\\Beehive Systems Ltd\\2009\\Wasp' 3D CombBuilder\\Templates\\CSharp"
"VSVBProjectTemplatesLocation"="D:\\Program Files\\Beehive Systems Ltd\\2009\\Wasp' 3D CombBuilder\\Templates\\VisualBasic"
"ProjectTemplatesLocation"="D:\\Program Files\\Beehive Systems Ltd\\2009\\Wasp' 3D CombBuilder\\Templates"
"AppName"="CombBuilder"
"VSTAVersion"="9.0"
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\CombBuilder\2.0\VSTA]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\CombBuilder\2.0\VSTA\InProcHost]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\CombBuilder\2.0\VSTA\InProcHost\{4A11F452-961F-4de9-9B80-019DABE5C56D}]
"FullClassName"="BeeSys.Wasp3D.CombBuilder.StateManagement.CombBuilderStateManagement"
"Assembly"="BeeSys.Wasp3D.CombBuilder.StateManagement, Version=1.0.0.0, Culture=neutral, PublicKeyToken=9f99f31d5dc9aca3"
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\SSIS_ScriptComponent]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\SSIS_ScriptComponent\2.0]
"AppName"="Integration Services Script Component"
"VSTAVersion"="9.0"
"ProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\component\\"
"VSCSProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\component\\CSharp\\"
"VSVBProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\component\\VisualBasic\\"
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\SSIS_ScriptTask]
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VSTAHostConfig\SSIS_ScriptTask\2.0]
"AppName"="Integration Services Script Task"
"VSTAVersion"="9.0"
"ProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\task\\"
"VSCSProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\task\\CSharp\\"
"VSVBProjectTemplatesLocation"="d:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Templates\\ssis\\scripting\\task\\VisualBasic\\"
Let me know if you need the Visual Studio 2008 registry hive as well.