I Have the same exact problem when encoding both H.264 and FLV, it seems like Adobe Media Encoder doesn’t decode the mov-file correctly, as is in the source window shows the frames as green, pixelated and garbled as in the above screenshot.
I wonder if the past 6 months have provided some solution?
I am running Adobe Media Encoder 5.0.1.0 (64-bit) on a MacBookPro 2.53 GHz Intel Core i5 with 4GB memory.
OS: OS X Snow Leopard 10.6.8
This is also messing up my workflow, and I fear going back to using Apple Compressor for making my h.264-files
Hope we figure this out!
-paul