This problem, as well as reset play counts, plagued me until I turned off the option to Show iTunes in the Cloud purchases (iTunes > Preferences > Store).
I have not had the problem since unchecking that box.
Others have also speculated that Genius could be a culprit as well. But I have not used the Genius feature in a year or so, so I can't say either way if it's to blame or not.
People in other threads have speculated that any kind of communications with Apple's servers can be at fault, including the Cloud, Genius, automatic downloads, sharing info with Apple, and even making store purchases.
It might very well be a combination of any of these (like maybe it could happen if you make a purchase but only if you have automatic downloads on). I don't know.
I have not experienced the problem since I turned the Cloud option off. Here are my current settings:
- Show Cloud purchases: off (turned off when I started having play count and metadata issues)
- Genius: off (never liked it, and it caused long sync times)
- Automatic downloads: off (just annoyed me; I want control of what to sync where and when)
- Share info with Apple: on (never thought about this option, so I left it alone)
And I have made quite a few purchases from the store with these settings and no ill effects.