Trouble syncing 2 iphones to 1 itunes library

[alanrobin1]

My wife and I both have the iphone and we are using the same itunes library on the Mac. The other day I was syncing her phone and all her folders on the phone were gone, but one and three out of 4 apps in that folder were on phone, but not in that folder. I then synced my phone and it went perfectly. She reestablished her folders on the phone and we plugged it again and this time, it looked ok on itunes until she hit apply and then 98% of apps were unchecked on itunes. Why is this happening to her alone and not me. It's frustrating not to mention the time to establish folders all over again.
Thanks for any help in this matter.
Alan