Where are these files coming from?
What exact version number of AE CS4 do you have?
This files are coming from a Panasonic AG-HPX500E camera. I have a CS4 9.03.8 AE.
I have the opportunity to test this in a AE CC and there isn't any problem about the DVCPRO HD 1080p files. It must be a bug in CS4 version. I have had to convert all the clips to AppleProRess before import them in my AE CS4.
Well, the good news is that you can try CC for 30 days so you can finish