Yup, I'd bet that's the problem.
You should also know that AECS4 does NOT play well with long-gop media containers like mp4 nor codecs like h.264... and since it's a iPhone, it's probably an mp4 file in the H.264 codec.
If you want true AE happiness, you'll have to transcode the file. AT Pro probably can do it (the PNG codec is great for this stuff). Adobe Media Encoder can probably do the trick as well.
CS4 was a lot less sophisticated dealing with H.264 and other MPEG flavors than current versions. As Dave said, convert it using external tools like Handbrake/ MPEGSTreamclip/ ffmpeg.