Importing geotagged jpeg and raw photos with xmp files issue

I had a folder of photos (all unique, no dupes) from two different cameras. Some were .jpg and some .cr2 (raw). I used an external app on my Mac 10.6.x called PhotoLinker to geotag the photos based on gpx track files. I wrote the metadata out to .xmp files, done by that app. So then I had a folder with .jpg, .cr2 and .xmp files I then moved them to another volume and did an Import Move operation in LR3. For the raw images, all went fine. The images were pulled into LR and they each had the geotagged data for location. But for the jpeg images they were imported into the catalog in LR but none of them had any geotagged data for the location.
Can someone let me know if they have encountered this problem and what they did about it? Is this a bug?
I even selected one of the JPG files in LR grid view, then did a read of the metadata from a file. The upper left corner displayed that the metadata file was being loaded from XMP. But again, no geotagged information. If I load that same .xmp file back into PhotoLinker it shows the geotagged data still there.
What gives? Why is this happening?
What I am using...
Mac OS 10.6.8
PhotoLinker 2.2.9
Lightroom 3.4.1

Thanks for the response and answer, Ian.
That strikes me as really odd. I realize that jpgs can have metadata within the image file and maybe the issue for LR is which does it consider to have priority. However, if so, why not present a dialog asking the user?
I would suggest Adobe plan on filling the gapping hole LR has when it comes to geotagging support. It currently provides very minimal support.

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OK, next RAW files again.
These hold the data the sensor 'saw' when you took the shot together with 'metadata' such as aperture, shutter speed, white balance settings, ISO setting etc - lots of data in fact.
Most programs do not alter RAW files at all - they are the digital negative and should not be altered.
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I said it was complex and confusing!
Continued again!
AC

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Importing geotagged jpeg and raw photos with xmp files issue

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