So Safari's and iBooks' aren't syncing? Also, magazines auto-downloading is up to the developers. I have 7 subscriptions and only a couple actually auto-download.
If Safari and iBooks is giving you problems, turn all of them off via Settings>iCloud and Settings>iBooks. Wait about 10 minutes and turn them back on.
Of course I have to ask, you are signed in with the same Apple ID, correct?