Metadata changed by another app?

After upgrading my 20K image library from 1.4.1 to 2.0, all of my photos show the 'The metadata for this photo has been changed by both Lightroom and another application. How should Lightroom synchronize this data?" flag on each photo.
This is odd because I've never used any other application on any of my photos nor have they been touched by anything other than LR.
My choices are:
Import Settings from Disk - will attempt to read the .xmp files that I don't use and, effectively, wipe out any and all adjustments and keywords I've added.
-or-
Overwrite Settings - will create .xmp files for each photo which I don't want to do. I prefer to just carry all metadata within the LR database rather than clutter my HDD with xmp files.
Any suggestions to help solve this dilemma are much appreciated.
-Dave

I had the same problem on a MAC a few weeks ago and posted it there with no result. I have also never used any external programs or had any sidecar files. I think it is a bug as it happened to all of my images before a certain date.
I managed to isolate it to a specific cause:
I use the import module to rename all my images on import with the date in the name and I always have done since LR 1.0beta. If you expand the metadata panel to show "all" you can see that there is a metadata field called "original filename" underneath the current file name. For images before some time in 07 - this field was not there and those are the ones that came up with the same metadata error flag symptoms that you have. Newer images which have an entry in that metadata field didn't come up with the error.
I suspect this means that older versions of LR import didn't update this field on a name change and somehow this has upset the metadata conflict check.
I couldn't find a way to resolve it without writing out 15k sidecar files which is clunky so I took the opportunity to rebuild my entire raw database as DNGs which has the side effect of curing the problem.

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