Compressor presets cropping video output - why?

Hi guys,
I've been using Final Cut Pro X for about a year now and was a heavy user of Final Cut Studio before that. I'd consider myself a fairly advanced user and i have a good understanding of workflows, encoding, etc. However, I am continually running into an extremely irritating issue when exporting video from Final Cut Pro X. I assume it isn't a bug, as it would be a pretty big one I'm sure would have been fixed by now. Wondering if I am just not understanding/missing something here:
When exporting via any of the Compressor presets (or modified variants of any of these) directly from FCPX, the resulting file is always cropped slightly on each side, almost as if a 2-3% zoom has been applied to the video before the final file is rendered out. Please note I also get the same result when exporting via 'send to Compressor' and using the same presets/modified presets.
This problem does not occur when I export a straight 'Master File' from Final Cut, but this obviously gives me an extremely large file that I then need to further compress before it is suitable for quickly sharing online (as I need to do with 99% of the videos I edit).
I've attached two screenshots of the same source exported:
1. Via exporting 'Master file' from FCPX's 'share' button.
1. Via exporting 'HD 720P' from FCPX's 'share' button (I get the same cropping result if I export via any of Apple's 'HD' presets, custom variants of these, or using any of the SAME presets directly from Compressor).
As you can see, with such screencast-type work I'm doing, the top pixels of the image really matter (icons and UI elements are cut off the top when this 'crop' occurs).
As far as I can see, this 'cropping bug' affects the HD 720/1080P output profiles. It does not happen when I export using the 'Apple Devices' h.264 presets.
Obviously there are ways to get around this, but all I really want for my workflow here is a quick way to export an h.264-encoded HD version of my source for quick uploading and sharing. Any help would be hugely appreciated, as this is about the only irritant in my workflow at this point!

Hah! I think you just got onto something there. Check out this shot of the same file open in QTX and QT7:
So it appears to me like QTX (and QuickLook) actually crop the edges off the file. Note that VLC also plays the video at the correct size.
I just took a look at this with a colleague of mine who works on the video encoding platform behind our product and we identified/confirmed the following:
- Some parameter or part of the data in the files being written by the HD 720/1080 compressor output is being read differently by QuickTime 7 and QuickTime X/QuickLook (which I think uses the QuickTime X rendering engine built-in to Mac OSX?). For some reason, the newer QT architecture reads these files as a cropped resolution.
- When I upload these files to our encoding platform and they are re-encoded using FFMPEG into
h.264 mp4 files (optimised for web streaming), FFMPEG also reads the resolution correctly, resulting in a new, encoded file that has the correct frame resolution.
So it seems we may have found the cause, but I suspect a solution is going to be a bit trickier, especiallty considering this isn't a problem that 'needs' solving.

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