Well, if it used to work... and then you updated your iphone and now it does not work... that seems to ME like the iphone update changed something in the files
But, exactly what is inside your mov files?
Read Bill Hunt on a file type as WRAPPER http://forums.adobe.com/thread/440037
What is a CODEC... a Primer http://forums.adobe.com/thread/546811
What CODEC is INSIDE that file? http://forums.adobe.com/thread/440037
Report back with the codec details of your file, use the programs below... a screen shot works well to SHOW people what you are doing
All Adobe updates start here and select product, read to see if you need to install updates in number order, or if the updates are cumulative for the individual product http://www.adobe.com/downloads/updates/
First, make sure you've got the latest version of Quicktime. Then make sure you've got at least 25-30 gigs of free, clean, defragmented space on your hard drive.
Beyond that, version 10 was only sporadically capable of working with MP4s from phone and iPods/iPads.
Version 11, however, handles this file format very well! If you're going to be shooting a lot with your phone or other non-camcorder camera, it will definitely be worth upgrading to it. You'll be amazed at how much easier it makes the whole workflow!
To the left of this page is my review and walkthrough of the new features.