I also have been experiencing wifi sync issues since ios6. I have an iPhone 4, an iPad 2 (?), a Macbook Pro (OSX Lion), and iTunes 10.7. Generally, iTunes sees the iPad upon startup, but has issues with the iPhone. Sometimes it's there, sometimes not. When it's not, I've tried powering off the phone, restarting Itunes, rebooting the Macbook, all of the above. Some things work sometimes, other times nothing works and I have to sync via USB. Even more annoying, sometimes iTunes sees the iPhone but I still can't initiate a wifi sync from the phone. I can usually initiate a wifi sync from iTunes, but that's inconvenient. Once I've successfully done a wifi sync from iTunes, I can usually do subsequent syncs (within an unknown time frame) initiated from the phone, but usually the scenario starts again the next day. There was a period of time where iTunes just wouldn't display the iphone under the left pane "Devices" section unless connected via USB, but now it does, but the phone still will not successfully initiate a sync more often than not. When the phone initiated sync fails, it times out and tells me the sync "will resume when <Macbook name> is available. So when iTunes can see the phone it appears the iphone has problems seeing iTunes.
I don't have a clue what's happening and the problem seems to be a moving target. As usual, Apple's silence on a definitive resolution is annoying and frustrating.
