Lightroom is changing metadata on imported photos

I imported a batch of RAW images into Lightoom 4.4 and see that a number of the images are displaying the icon warning that metadata has been changed in Lightroom although the affected images have only just been imported into the catalog and I have not made any changes to them. 130 images out of a batch of 300 are being affected.
I have selected the affected images and re-read the metadata using Metadata / Read Metadata from File, but within a couple of minutes of being re-read, the metadata changed icon has reappeared.
My initial thoughts were that I had changed one of the preferences and something was being automatically applied, but if that was the case then I would have expected it to be applied to all 300 images in the batch which were taken on the same day on a single camera. I've created a smart collection to identify images with metadata changed in Lightroom and find that they appear to be randomly spread through the catalog affecting both RAW images and jpegs from 3 different cameras.
In order to exclude any changes to Lightoom preferences I may have made, I installed Lightroom 4.1 on another PC and created a new catalog using the default settings. I then imported the same batch of 300 RAW images and confirmed that the same ones displayed the warning icon that metadata was changed in Lightroom .
Can anyone explain what might be causing this?
The PCs are Windows 7 Professional, Lightroom 4.4 (Lightroom 4.1 on the test PC), RAW files are from Nikon D90 and D7100 cameras.
Thanks

I agree with most of your points:
Points 1, 2, 3 - I agree.
Point 4.
yes - all of my RAW files have .xmp files associated with them as they contain the metadata and keywords I have entered via Bridge/ACR.
Lightroom imports these details but shouldn't then be making any additional changes which need to be written back to the xmp files. This is where the problem has surfaced as Lightroom has made unknown changes to some of the photos and wants to write them back to the xmp files - see my comments below about point 6.
Point 5.
By installing a trial copy of Lightroom 5.3 on a different PC and creating a new catalog I avoided carrying forward any incorrect preferences etc I may have previously used - all photos in this new catalog have been freshly imported for testing. The fact that Lightroom displays the "metadata has changed" icon to the same photos as my original Lightroom 4.4 installation after importing them demonstrates that an unidentified Lightroom process is making changes to some (but NOT ALL) of the imported photos.
The problem is identifying WHAT Lightroom has changed and the implications of these changes.
Point 6.
"auto write to xmp" - This is not selected in my catalog settings as I want to be in control of when Lightroom updates the xmp files. At present I am still learning Lightroom so I don't want to accidentally write any changes back to the xmp files until I am completely sure of the consequences, hence my main work still takes place in ACR.
Point 7.
My current workflow choice is to continue using xmp sidecar files as per the following statement at
http://www.adobe.com/uk/products/photoshop-lightroom/faq.html
"Changes you make in Lightroom can appear in Camera Raw and vice versa. To complete this interactivity, changes in both Camera Raw and Lightroom need to be written to XMP metadata. This is so that each software application can recognize the other's edits."
- but I have to be confident that any Lightroom changes to the xmp files are as a result of my planned actions.
Point 8.
All of the default Develop Settings are deselected in my preferences/presets and I don't have any import presets - the develop settings and metadata are set to "none".
Do you have any suggestions on how to identify what changes Lightroom has made to the photos where it has set the "metadata has changed" icon?

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