I have this problem taking DVCProHD 720p60 files from my client who uses FCP when I output from After Effects CS4 – gamma is incorrect, blown out, etc. If I output a ProRes from AE using the original DVCPro file as a source FCP and Color interpret the ProRes fine.
As a VFX vendor, I’ve worked with the MXF DVCPro format with After Effects before and I’ve never had this problem, although the client at the time captured and edited in Premiere Pro, and I believe it was in Windows :\