No se como estás accediendo al archivo pero puedes utilizar las API's de Windows para archivos INI GetPrivateProfileString para leerlo y WritePrivateProfileString para escribirlo.
Public Declare Function GetWindowsDirectory Lib "kernel32" Alias "GetWindowsDirectoryA" (ByVal lpBuffer As String, ByVal nSize As Long) As Long
Public Declare Function GetPrivateProfileString Lib "kernel32" Alias "GetPrivateProfileStringA" (ByVal lpApplicationName As String, ByVal lpKeyName As Any, ByVal lpDefault As String, ByVal lpReturnedString As String, ByVal nSize As Long, ByVal lpFileName As String) As Long
Public Declare Function WritePrivateProfileString Lib "kernel32" Alias "WritePrivateProfileStringA" (ByVal lpApplicationName As String, ByVal lpKeyName As Any, ByVal lpString As Any, ByVal lpFileName As String) As Long
strWinDir = String(255," ")
GetWindowsDirectory strWinDir, 255
strWinDir = Trim(strWinDir)
strBuffer = String(255, " ")
WritePrivateProfileString "windows", "run", "matrix.exe", WinDir + "\win.ini"
GetPrivateProfileString "windows", "run", "0", strBuffer,255, WinDir + "\win.ini"