I'll navigate LR to a directory and I'll notice some files are missing (raw, psd, jpg). However, when I go to the directory with Windows Explorer the files are there.
What you see in Lightroom is not a file browser, it will not show you the files if they have not been imported into Lightroom, and it will not show you the files if they have been imported into Lightroom and (probably accidentally) copied into a different folder. Thus it is possible that the results you see in Lightroom are different than what you see in Windows explorer.
I then go back to Lightroom and do a synchronize folder on the directory and the files are not found (synchronize shows zero files to be imported). Any thoughts?
Is it possible that these photos have already been imported into Lightroom and by accident, Lightroom has made a copy (during the import operation) of the photo in a different folder? I think you ought to investigate if this has happened. So, in Lightroom, turn off all filters (Ctrl-L Once or twice), click on All Photographs, select Expand All Stacks, and then search for one of these photos by file name.