Depois de fazer muitas pesquisas e tentar encontrar a raiz do problema testando soluções relacionadas, corrigi meu problema com esse script de registro que corrige a associação de arquivos .lnk:
Nota: É para o Windows 8 / 8.1
Windows Registry Editor Version 5.00
; Created by: Shawn Brink
; http://www.eightforums.com
; Tutorial: http://www.eightforums.com/tutorials/8486-default-file-associations-restore-windows-8-a.html
[-HKEY_CLASSES_ROOT\.lnk]
[HKEY_CLASSES_ROOT\.lnk]
@="lnkfile"
[HKEY_CLASSES_ROOT\.lnk\ShellEx\{000214EE-0000-0000-C000-000000000046}]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\.lnk\ShellEx\{000214F9-0000-0000-C000-000000000046}]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\.lnk\ShellEx\{00021500-0000-0000-C000-000000000046}]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\.lnk\ShellEx\{BB2E617C-0920-11d1-9A0B-00C04FC2D6C1}]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\.lnk\ShellNew]
"NullFile"=""
"IconPath"=hex(2):25,00,53,00,79,00,73,00,74,00,65,00,6d,00,52,00,6f,00,6f,00,\
74,00,25,00,5c,00,73,00,79,00,73,00,74,00,65,00,6d,00,33,00,32,00,5c,00,73,\
00,68,00,65,00,6c,00,6c,00,33,00,32,00,2e,00,64,00,6c,00,6c,00,2c,00,2d,00,\
31,00,36,00,37,00,36,00,39,00,00,00
"ItemName"="@shell32.dll,-30397"
"Handler"="{ceefea1b-3e29-4ef1-b34c-fec79c4f70af}"
"MenuText"="@shell32.dll,-30318"
[HKEY_CLASSES_ROOT\.lnk\ShellNew\Config]
"DontRename"=""
[-HKEY_CLASSES_ROOT\lnkfile]
[HKEY_CLASSES_ROOT\lnkfile]
@="Shortcut"
"NeverShowExt"=""
"EditFlags"=dword:00000001
"IsShortcut"=""
"FriendlyTypeName"="@shell32.dll,-4153"
[HKEY_CLASSES_ROOT\lnkfile\CLSID]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\lnkfile\shellex\ContextMenuHandlers\OpenContainingFolderMenu]
@="{37ea3a21-7493-4208-a011-7f9ea79ce9f5}"
[HKEY_CLASSES_ROOT\lnkfile\shellex\ContextMenuHandlers\{00021401-0000-0000-C000-000000000046}]
@=""
[HKEY_CLASSES_ROOT\lnkfile\shellex\DropHandler]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\lnkfile\shellex\IconHandler]
@="{00021401-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\lnkfile\tabsets]
"selection"=dword:00000705
[-HKEY_CLASSES_ROOT\SystemFileAssociations\.lnk]
[HKEY_CLASSES_ROOT\SystemFileAssociations\.lnk]
"FullDetails"="prop:System.PropGroup.Description;System.ItemTypeText"
"FileOperationPrompt"="prop:System.ItemTypeText;System.FileOwner;System.Author;System.Title;System.Subject;System.Comment;System.DateModified;System.Link.TargetParsingPath"
[-HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\FileExts\.lnk]
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\FileExts\.lnk\OpenWithProgids]
"lnkfile"=hex(0):