Incorrect rotation for imported photos

Greetings,
I just bought a new iMac from a retail Apple Store today, and I wanted to migrate all of my photos from my Windows 7 PC to the iMac. First, I updated all of the software on the iMac to the latest versions. I copied all of the photos (about 4,000) from the PC to a USB thumb drive. I inserted the thumb drive into the iMac. Then I opened iPhoto and imported all of the photos from the thumb drive.
The problem is that many of the imported photos display in iPhoto with the incorrect orientation. They all look correct on the PC.
I can't perceive a pattern as to which photos are rotated correctly and which are rotated incorrectly. My photo collection contains a mix of portrait and landscape photos, and I can find examples of both types which are rotated correct and incorrectly.
If I select one of the incorrectly rotated photos and click File->Reveal in Finder->Original File, interestingly, the thumbnail for the file appears correctly rotated in the folder. If I open the file, it appears incorrectly rotated in the preview. Clicking File->Reveal in Finder->Modified File produces a file with an incorrectly rotated thumbnail.
Because I'm dealing with over 4,000 files, the number of incorrectly rotated photos is in the hundreds, so I really don't want to go through my entire library and manually rotate the bad ones. Any help is much appreciated.

After some experimentation, I think I tracked down the cause:
Today on my PC, I tried running a lossless auto-rotater program on all of the photos. Sure enough, many of the photos that previously appeared to be rotated correctly were rotated incorrectly by the auto-rotater. These incorrectly rotated photos match the incorrectly rotated photos in iPhoto on the Mac. All of the incorrectly rotated photos seemed to be dated from 2007 or earlier. I vaguely recall using some third-party app on an older PC back then that would automatically extract photos from my camera and losslessly auto-rotate them. My suspicion is that this app would rotate the photos without correctly adjusting the orientation component of the EXIF data.
My solution was to browse through all of the photos caught by my auto-rotater and fix them manually. Since they were all from 2007 or older, it wasn't so bad to go through all of them.
Thanks to everyone for the help. You were clearly on the right track.

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