I was having a similar but different problem. I ran a search and found this thread.
I have the latest iTunes on a late 2010 MacBook Air, an iPhone 5 and a new iPad Air. In iTunes, I enabled "Sync over wifi" for both the iPhone and iPad. When I open iTunes, it will wirelessly recognize both devices - most of the time. iTunes will always "see" the iPhone, but not always the iPad. At that point, the only way to sync the iPad is to plug it into the Mac via USB. Then, iTunes will see both devices.
After being connected to iTunes this way, I can unplug the iPad and both devices awe still listed as connected. This works for a while, but I still occasionally lose the wireless connection to the iPad.
Any solution would be appreciated.
Ryan