Man, I wish I knew what it could be. It's odd that your computer would just remove contacts, especially if you aren't syncing them with it. Have you tried using iCloud? I personally do and I absolutely love it for syncing contacts. All of mine are in sync across my Mac, iPad, iPhone and iPod. The only downside I've seen it has occasionally duplicated a contact and when I remove the dup, it removes all entries for that user. Luckily the 2 times it's happened, I had my contacts also stored somewhere else.