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I need a sample image which has been edited with iView to comment on this. CR2 is TIFF-based, and if iView is using the standard TIFF method of adding information then there is no problem. Utilities which do things like adding proprietary-format information to the end of the file cause headaches. (This is how Canon's own DPP stores information.)
The conflict with PhotoMechanic was simply that it moved the main TIFF IFD to the end of the file. It was using the standard TIFF format, but ExifTool was using the IFD location as part of the logic to identify a CR2 image. I have since relaxed this constraint, and now only test the 4-byte "magic number" in the header of the file. The problem is that if the image isn't properly identified and is edited as a standard TIFF, there are 2 pieces of information that are lost: 1) The 4-byte CR2 "magic number" in the header, and 2) the DPP trailer if edited by Canon's utilities.
BTW. What version of OS X are you running? Is there still a problem with the Apple utilities reading CR2 images that have been edited by ExifTool? I have heard a rumour that Apple fixed this, but I would like to know for sure. I'm stuck on 10.3.9 so I can't test this myself.
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