ITunes not re-installing apps after restore

Anyone having a problem where iTunes is failing to re-insall apps after a carrying out a restore? I backed up my phone before carrying out the restore, once the restore is complete everything is re-installed except apps. I have to then manually place them back on my phone.

Yeah I carry out a sync before doing my restore, the Apps I want are ticked. After doing the restoring my device iTunes then offers me the option to restore from either my last sync (today it was the one before restore was carried out) or previous ones. I choose today's and then it starts to place back everything but Apps. Then after the restore sync was completed, I saw my apps folders (which I created) there and every app I have had on the side. That's when I have to manually place them back. Where do you think I'm going wrong so I know next time what to do? It's only happening recently, I've never had this problem before with restoring.

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