I've seen this type of behavior before, but it was tracked changes that were the culprit. However, they were not easily found. In InDesign I believe that tracked changes had been turned off, but not all changes were accepted. I think to solve it the customer opened it in InDesign, turned tracked changes back on and then accepted all changes.

Regardless the frustrating part is that the setting in the file type that allows you to allow tracked changes does not work. We filed a bug a while ago with SDL on this issue.

One way you can determine if tracked changes are your culprit is by unzipping the idml (you can rename it to .zip. Then in the files there you'll find some stories files. In those files if you have any change elements, then tracked changes is your problem. Specifically when the changes are nested withing each other like

<change>
content
<change>
more content
</change>
yet more content
</change>

In the example above, in my testing the "more content" section would not show up in studio.

Hope this helps

Starting simple, are the content of these missing pages on a locked layer? We've had issues where the content in locked layers are not processed in Studio.