Without knowing your exact conversion settings this sin't going anywhere. Most likely you simply chose unsuitable settings and as a result ended up with an out-of-spec MP4 file that AE just doesn't like.
I'm pretty new to the AE interface, so I don't understand what you mean by "conversion settings".
You said you converted the FLV to MP4. We need to know how you did that.
Also, why did you choose that workflow? MP4 is not a good intermediate format.
I'm with Szalam on this. Instead of MP4, try transcoding to a Quicktime movie in the Photo JPEG codec. I bet the problem goes away. If it doesn't, you have more fundamental issues.