Apple ProRes 422 from FCP X and FCP 7 give different results!

Our workflow uses Compressor 3 to generate PAL files in H.264 format for transfer to other locations. For several years, we have been using the same settings (part of a batch file) that we run to generate all the necessary variants of our self-contained Apple ProRes 422 video. Most times, we will only use part of the batch file - removing what we don't need.

Yesterday, after making the ProRes 422 file using FCP X and then batching the PAL / H.264 format video with Compressor 3, the time required to convert this 30 minute video (usually around 1 hour) was looking to exceed 6 hours - this before we terminated the batch. Lowering some of the video settings helped slightly.

We imported the FCP X, ProRes 422 file into FCP 7 and then rewrote it to another file as a ProRes 422 file. Same settings, timing, etc. The result was that Compressor 3 made the requisite PAL H.264 file in about 1 hour - just like before - with the video settings for "Best" quality compensations.

From the file info, the slight variations are as follows:

Based on the significant differences in the way Compressor 3 behaved with these two files, the FCP 7 generated from the FCP X file, I can only conclude that there is a difference in the way the Apple ProRes 422 Codec has been implemented.

Has anyone else experienced this?

Is there something I can / should do to fix the problem with the conversion?

Is this a reason to use Compressor 3 with FCP 7 and Compressor 4 with FCP X? (I do not have Compressor 4 as I didn't see a need for it)!

Suggestions, help would be appreciated!