Resylenr, разобрался в чём дело и нашёл ошибку. Правда, прежде пришлось самому пересобрать программу
Код:

Root: HKLM; SubKey: SOFTWARE\Classes\jpegfile\shell\edit\command; ValueType: string; ValueData: "\""{app}\PaintDotNet.exe\"" \""%1\"""; Flags: uninsdeletevalue
должно быть, так:
Код:

Root: HKLM; SubKey: SOFTWARE\Classes\jpegfile\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletevalue
исправьте все строки в соответствии с этим и будет у вас счастье...
P.S.
Если интересно, я вношу в реестр немного другие изменения, вот мой пример скрипта
читать дальше »
[Setup]
AppName=Paint.NET
AppVerName=Paint.NET 3.36
VersionInfoVersion=3.36
AppPublisher=dotPDN LLC
AppPublisherURL=http://www.getpaint.net
AppSupportURL=http://www.getpaint.net
AppUpdatesURL=http://www.getpaint.net
DefaultDirName={pf}\Paint.NET
UninstallFilesDir={app}\Uninstall
DefaultGroupName=Paint.NET
AllowNoIcons=yes
ChangesAssociations=yes
InfoBeforeFile=Paint.NET\License.txt
OutputDir=D:\Мои сборки
OutputBaseFilename=Paint.NET
SetupIconFile=C:\Program Files\Иконки\41.ico
UninstallDisplayIcon={app}\PaintDotNet.exe
Compression=lzma
SolidCompression=yes
[Languages]
Name: russian; MessagesFile: compiler:Default.isl
[Tasks]
Name: desktopicon; Description: {cm:CreateDesktopIcon}; GroupDescription: {cm:AdditionalIcons}; Flags: unchecked
Name: quicklaunchicon; Description: {cm:CreateQuickLaunchIcon}; GroupDescription: {cm:AdditionalIcons}; Flags: unchecked
[Files]
Source: Paint.NET\*; DestDir: {app}; Flags: ignoreversion recursesubdirs createallsubdirs
Source: Sys32\wiaaut.dll; DestDir: {sys}; Flags: onlyifdoesntexist regserver sharedfile
[Icons]
Name: {commonprograms}\Стандартные\Paint.NET; Filename: {app}\PaintDotNet.exe; WorkingDir: {app}; Comment: Бесплатный графический редактор Paint.NET 3.36
Name: {commondesktop}\Paint.NET; Filename: {app}\PaintDotNet.exe; WorkingDir: {app}; Comment: Бесплатный графический редактор Paint.NET 3.36; Tasks: desktopicon
Name: {userappdata}\Microsoft\Internet Explorer\Quick Launch\Paint.NET; Filename: {app}\PaintDotNet.exe; WorkingDir: {app}; Comment: Бесплатный графический редактор Paint.NET 3.36; Tasks: quicklaunchicon
[UninstallDelete]
Type: filesandordirs; Name: {app}\*
[Registry]
Root: HKLM; SubKey: SOFTWARE\Classes\.bmp\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.jpe\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.jpeg\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.jpg\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.pdn; ValueType: string; ValueName: ; ValueData: Paint.NET.1; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.pdn; ValueType: string; ValueName: PerceivedType; ValueData: Image; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.pdn\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.png\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.tga; ValueType: string; ValueName: Content Type; ValueData: image/targa; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.tga; ValueType: string; ValueName: PerceivedType; ValueData: Image; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.tga; ValueType: string; ValueName: ; ValueData: Paint.NET.1; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\.tga\OpenWithProgids; ValueType: string; ValueName: Paint.NET.1; ValueData: ; Flags: uninsdeletevalue
Root: HKLM; SubKey: SOFTWARE\Classes\Applications\PaintDotNet.exe\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Applications\PaintDotNet.exe\shell\open\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Applications\PaintDotNet.exe\shell\print\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""print:%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\jpegfile\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Paint.NET.1; ValueType: string; ValueName: ; ValueData: Paint.NET Image; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Paint.NET.1\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Paint.NET.1\shell\open\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Paint.NET.1\shell\print\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""print:%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\Paint.Picture\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Classes\pngfile\shell\edit\command; ValueType: string; ValueData: """{app}\PaintDotNet.exe"" ""%1"""; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: CHECKFORUPDATES; ValueData: 1; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: TGAEDITOR; ValueData: 1; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: JPGPNGBMPEDITOR; ValueData: 1; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: TARGETDIR; ValueData: {app}\; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: USINGWIZARD; ValueData: 1; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: LASTACCEPTEDEULAVERSION; ValueData: 20080601; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: PDNUPDATING; ValueData: 0; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: SKIPCLEANUP; ValueData: 0; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: QUEUENGEN; ValueData: 1; Flags: uninsdeletekey
Root: HKLM; SubKey: SOFTWARE\Paint.NET; ValueType: string; ValueName: LanguageName; ValueData: ru-RU; Flags: uninsdeletekey