Catalog partially and randomly synced with disc. Have to find and sync A LOT.  Help!  :(

I am just getting started with LR4.  After installation, the catalog is only partially and randomly synced with my hard drive. (Windows 7)  It seems I have to find and sync way too many files.  There are some files which don't appear in the catalog at all.  So I uninstalled and reinstalled the program and the problem is the same.  Did I miss something or do I have a corrupt program?  Can I find and sync my entire pictures file at once?

Well, that's a clear indication that the files in question indeed are alreaday somewhere in your catalog; Lightroom is usually right about that. They might not be in the place you expect them to be though.
You might want to look carefully through the folder structure in Lightroom and see if there are any strange folders you don't remember creating.
One thing that might have happened during one of the imports is that instead of choosing 'add' in the import window, you had 'copy' selected. When doing that, files end up in the place defined in the right hand column of the import window. Depending on what was selected (or what was there as default), LR has created a folder e.g. with the date of the pictures as name, inside an other folder, etc.
I encountered this kind of problem myself. An example of what happened:I have my files in folders named by date, in hierarchical year-month-day structure. Using the 'Import' function, I wanted to 'add' the '2011-05-12' to my '2011-05' folder, but erroneously selected 'copy'. Due to the selection I made last time I 'copied' files on import, the folder ended up in the folder '2011-04' - which I didn't notice at first. After the import, I couldn't find the 2011-05-12 folder, and when trying to import the whole 2011 folder with all of its subfolders, it told me that there are no pictures to import as all were already in the catalog. Like in your case, only unchecking 'don't include suspected duplicates' let me see the missing files.
So try to see if you can find folders where they shouldn't be or folders with unusual names. If that's the case, remove them from the catalog, and your problems will disappear.

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