Is this broken or what?

Yes I know what caused it. You took ownership of your appdata folder.

See:

Stop Application Data folder replicating?

Stop Application Data folder replicating?

Also see here for links:

Infinite Application Data

As far as I know System32 is not affected. For anyone else reading this - do not take ownership od System32.

You can edit the default junctions list that affects what will be restored when you run the program (in theory) - I haven't tried manually editing the file.

DefaultJunctions.ntj

Code:

; A list of the standard set of junctions in Vista and Windows 7, for repair purposes.
;
; Notation is as follows:
;  Section headers refer to userprofile-folders unless otherwise indicated by a full path.
;  Paths beginning with a \ indicate a fully-qualified path from the systemroot. (Typically C:\)
;  Paths beginning with @ are relative to the profile container. (Typically C:\users)
;  Junction location and target paths are relative to the section-header [value] unless qualified.
; The Default profile settings will be applied to all generic users when profiles are repaired.
; You may add custom sections for specific users, though this is not normally necessary.
; Wildcards or macros other than those stated above are not permitted.
; Junctions will be created using full target-paths, irrespective of relative or full values here.
; Note: Non-English users will need to create their own file, sorry.

[General]

; Displays warning if incompatible OS or system-language is found.
OSVersions=WIN_VISTA,WIN_7,WIN_2008,WIN_2008R2,WIN_LONGHORN
OSLanguages=0409,0809

; Force the creation of junctions in system or user folders, or both.
; =1 recreates (parts of) profile folder-structure if missing. Relatively safe to use.
; =2 forcibly deletes any file, folder or junction occupying the target location. 
; -valuable when dealing with corrupt junctions, but use with care as may delete data.
; Default is to leave existing junctions alone and only add missing ones, but set correct permissions on all.
SystemForceCreation=0
UserForceCreation=0

; The following sections refer to disk folders and the required junctions in each, as JunctionName=JunctionTarget.

[\]
Documents and Settings=@

[\ProgramData]
Application Data=\ProgramData
Desktop=@\Public\Desktop
Documents=@\Public\Documents
Favorites=@\Public\Favorites
Start Menu=Microsoft\Windows\Start Menu
Templates=Microsoft\Windows\Templates

[@]
Default User=Default

[All Users]
Application Data=\ProgramData
Desktop=@\Public\Desktop
Documents=@\Public\Documents
Favorites=@\Public\Favorites
Start Menu=\ProgramData\Microsoft\Windows\Start Menu
Templates=\ProgramData\Microsoft\Windows\Templates

[Public]
Documents\My Music=Music
Documents\My Pictures=Pictures
Documents\My Videos=Videos

[Default User]
; (intentionally blank)

[Default]
Application Data=AppData\Roaming
Cookies=AppData\Roaming\Microsoft\Windows\Cookies
Local Settings=AppData\Local
My Documents=Documents
NetHood=AppData\Roaming\Microsoft\Windows\Network Shortcuts
PrintHood=AppData\Roaming\Microsoft\Windows\Printer Shortcuts
Recent=AppData\Roaming\Microsoft\Windows\Recent
SendTo=AppData\Roaming\Microsoft\Windows\SendTo
Start Menu=AppData\Roaming\Microsoft\Windows\Start Menu
Templates=AppData\Roaming\Microsoft\Windows\Templates
AppData\Local\Application Data=AppData\Local
AppData\Local\History=AppData\Local\Microsoft\Windows\History
AppData\Local\Temporary Internet Files=AppData\Local\Microsoft\Windows\Temporary Internet Files
Documents\My Music=Music
Documents\My Pictures=Pictures
Documents\My Videos=Videos

If you took ownership of System32 and subfolders then that will really screw things up

I think you need a "permissions" expert to advise.

john1955 said:

Anything that's a *shortcut* I cannot access (but not many are shortcuts) but now I cannot access C:\ProgramData\ApplicationData

That's how it should be:

Good Luck! :)