How does metadata get changed by both Lightroom and another application??

I am frequently getting the message "The metadata for this photo has been changed by both Lightroom and another application. Should Lightroom import settings from disk or overwrite disk settings with those from the catalog?" on images in my catalog. I use only Lightroom to organize, add keywords, do basic adjustments, etc. On the occasions I am taking an image into Photoshop to do further work, it's exported as a TIFF or PSD and the original stays in the LR catalog untouched by anything else I might do to the image.
I have two choices with this message: Use Lightroom's settings, OR overwrite them from disc. The first few times this scared me, as I had no idea where those changes were coming from and why the disc file had something different than the lightroom catalog. I have all my metadata saved in XMP files. But I took the chance and said overwrite LR settings, and saw nothing change on the sliders or image being displayed. I then tried a few saying 'keep LR settings', and again I saw no visible signs of changes. That leads me to believe that they are NOT changed but LR things they are somehow. But I don't like seeing it, I want it to go away unless there really are changes happening outside of LR (like if I went into Bridge or something...)
Any ideas why this message shows up? I just discovered about 100 images in a collection of images I sent to stock agency three years ago, and haven't done anything with them outside of LR since.
Thanks for any help you can give.

Users have complained for years about spurious metadata-has-changed notifications. If you're confident that you're not editing the file itself outside of LR, then choosing Overwrite Settings will rewrite the metadata in the file with the catalog metadata and (usually) make the spurious notification go away.
Unfortunately, LR doesn't tell you which metadata fields have changed, so users are left flying blind. I believe Rob Cole had a plugin that would tell you metadata differences between the catalog and the disk file, but his Web site has been down for a couple of weeks now.
ManiacJoe: My guess is that Photoshop is updating some EXIF data fields in the raw file, for example the "edited with software" field. Since Lightroom probably has already set that field, it gives you a warning that something changed.
Interesting hypothesis. I just tested that with LR 5.7.1, Photoshop CC 2014, OS X 10.10 and couldn't reproduce the problem. I exported a TIFF from a cataloged raw file into the same folder as the raw, edited the TIFF and changed some of its metadata in Photoshop, and saved it. LR didn't report a metadata-has-changed notification.
In general, I'd be (only moderately) surprised that if you edited x.tif in PS, it would change any metadata in x.cr2 or x.xmp.

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Often, I am not sure how to answer that one. Usually, I'm not aware of having made any changes explicitly, either in Lightroom, or externally when I get this prompt. Generally what I'm dieing to know when I see this is:
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A feature that could show me what the difference is between the on-disk metadata and the in-catalog metadata would be most appreciated.
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