Illustrator substitutes fonts when opening document without warning.

Since no answer was correct and I was having the same trouble and only found this thread, even if the original post is 9 years old, here's the answer for anyone who needs it:

Go to "Type > Resolve missing fonts" and in the dialog, uncheck "Don't show on document open"

Try it:

// fonts to replace
var substitutions = [
  ['Myriad Pro', 'Regular',        'Times', 'Regular'],
];

//  turn the substitutions into real fonts
var subsRight = [];
var fontCount = textFonts.length;
var subsCount = substitutions.length;
for (var i = 0; i < fontCount; i++) {
  var font = textFonts;

  for (var j = 0; j < subsCount; j++) {
    if (substitutions[2] == font.family && substitutions[3] == font.style) {
      subsRight = font;
    }
  }
}

function getAllFiles(folder) {
  var fileList = [];
  function recurse (folder) {
    var files = folder.getFiles("*.ai");
    for (var i = 0; i < files.length; i++)
      fileList.push(files);


    var folders = folder.getFiles();
    var len = folders.length;
    for (var i = 0; i < len; i++) {
      if (folders instanceof Folder) {

        recurse(folders);

      }
    }
  }
  if (folder != null && folder instanceof Folder)
    recurse(folder);
  return fileList;
}

var sourceFolder = Folder.myDocuments.selectDlg( 'Select the folder with Illustrator files in which you want to replace fonts');
var files = getAllFiles(sourceFolder);

for ( var i = 0; i < files.length; i++ ) {
  var file = files;

  var doc = app.open(file);

  // replace the font
  var frames = doc.textFrames;
  for ( var j = 0; j < frames.length; j++ ) {
    var ranges = frames.textRanges;
    for ( var k = 0; k < ranges.length; k++ ) {
      var range = ranges;
      for (var f = 0; f < subsCount; f++) {
        if (range.characterAttributes.textFont.family == substitutions[0]
          && range.characterAttributes.textFont.style == substitutions[1]) {
          range.characterAttributes.textFont = subsRight;
        }
      }
    }
  }
  redraw();
}

If I may add some other suggestions besides what Tom & Mario have said:

Check to see if your Illustrator has any auto-activation plugs installed, such as what Suitcase adds.

I'm a firm believer in not using any auto-activation stuff, and driving my own car. One never knows what those things do.

You claimed that you tested this with Suitcase, Universal Type server and Font Explorer. Are these on different work stations or all on one computer? You're asking for trouble if you have more than one font management software installed on one machine; they could be conflicting with each other. That goes for Mac's own Font Book.app. (Either trash this program or .zip it up and trash it's preferences) Use only one!

You can also search your computer and delete any old "adobefnt*.lst" files (with * being a number). These are list files that Adobe uses, but are like preferences that you can safely delete and they will be rebuilt.

Here is a link that you may also find helpful for font troubles:

http://kb2.adobe.com/cps/327/327791.html

and I've found this piece by Kurt Lang invaluable:

http://www.jklstudios.com/misc/osxfonts.html

Yeah, this is very big and money cost problem, happened to me a few times and couldnt find and answer. To try to prevent this  I did this two posible options, but is not perfect...

1. There is an option under the page setup uncheked by default named "Highlight substitude fonts" so you have to check this option for every document you have and make, what a nightmare, this must be checked by defalut, please adobe team...!

2. Also yo can try to change the default font following this steps, another nightmare because not always work

To change the default font for Illustrator CS4

1. Choose  File > Open and go to Documents and Settings/User/Application  Data/Adobe/Adobe Illustrator CS4 Settings/New Document Profiles  (Windows) or to Users/User/Library/Application Support/Adobe/Adobe  Illustrator CS4/New Document Profiles (Mac OS).
2. Open  one of the default document profile template files (Basic CMYK, Basic  RGB, Mobile and Devices, Print, Video and Film, or Web, depending on  which type of document you intend to use).
3. Choose Window > Type > Character Styles.
4. Select the Normal Character Style and choose Character Style Options from the palette menu.
5. Select Basic Character Formats and choose the desired font from the Font Family menu.
6. Click OK, and then choose File > Save and close the file.
7. Restart Illustrator

Give it a try and tell us..

If you're not getting any Warning, I would go to Preferences and Reset All Warning Dialogs.