Sounds like you have a configuration issue with either a AD sync or your User Profile Manager.
There is a timer job that runs and tries to link each mysite with a owner, if it doesn't find it, it starts the clean up. This is basically the thing that will delete the "My Content". Other data will remain in the sync process.
Read up here: http://technet.microsoft.com/en-us/library/ee624362%28v=office.14%29.aspx
You may need to change the timer job times to be away from your AD sync as they may be conflicting and/or they aren't being resolved properly in AD / with the UPM.
You should look for things to do with this timer job in the ULS to see what is going on.
This won't be a straight forward fix, but potentially playing with the timer jobs timing could present a temporary fix, or even disabling it entirely.