Specific Files Deleted from All Time Machine Backups

Greetings all!
I hope you may be able to solve my problem here. Today I purchased a new late-2013 iMac 3.2 GHz i5, running OSX 10.9.3. I've had several computers this year and chose not to restore from my many backups, but rather transferred all documents, data, settings, etc. from my latest backup (completed today, which I know had all the original files) via Migration Assistant. Upon completion, I noticed that many of my folders and files were missing! My first response was to simply check my month-long list of backups for those specific folders and they were all missing as well. This came as quite a scare, as I run a design business and this is my main backup. Note: these are not files that would be on the list that Time Machine skips over; they're just my regular files (docs, pics, pdfs, etc.).
Now, in a few of the backups, in my User folder, there are more folders than others, along with a few seemingly random files (i.e. company A -> contracts -> onlyme.pdf), but the rest of the files are missing! Some backups include the main Music, Pictures, Documents, etc. and some only include a few. I've verified and repaired the disk, but this only made more files vanish from the backups! I have hidden files visible, which also has not helped. Is there something I'm missing? Disk permissions on Disk Utility are greyed out and I don't know of any other options. Can anyone advise? Are these files simply lost forever?
Thanks in advance!
Tim

If repairing the volume caused more files to disappear, then the drive is malfunctioning and must be replaced. That's why one backup is not enough to be safe. You need at least two independent backups on different storage devices.

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