I think more info is needed. It’s normal for peak levels to increase when converting a WAV to AAC. If you don’t leave enough headroom on a mastered WAV file, you might see clipping on the resulting AAC file. It’s normal. It’s very possible for WaveLab to not report any clipping (because there is no clipping), but still to have clipping after the WAV is converted to AAC. This is entire reason to have these testing tools. Peak levels increase on mp3/ACC encoding as well as sample rate conversions. You need to find an output ceiling level that survives the encoding process.
Some people set the output ceiling as low as -1.0dBFS and their master WAV files, and it can be helpful to use a true peak limiter rather than just a digital peak limiter.
The funny thing about Mastered For iTunes if you read the manual is Apple says this:
"iTunes won’t reject a master file based on the number of clips the file contains. This tool is provided so you can make an informed decision about whether to submit an audio file or go back to the drawing board and make adjustments. It’s a creative decision— one that’s entirely up to you."
So while they recommend that your master WAV files don’t result in clipped AAC files, they still allow it.
I think the Apple supplied tools are garbage though, especially the one that runs live like a plugin. You’ll get differing peak results on each playback because the playback is not in sync with the codec buffer.
To get accurate results, you must do it in an offline process like the Sonnox Pro Codec Manager app does. Offline testes will give you repeatable results. Live playback will not.
With the OS X Terminal I believe you can do some offline tests but I have never tried it. There is more info in the MFiT manual about it:
The main answer I think is that if you’re seeing clipping on the AAC files, you need to lower the output ceiling of the final limiter in WaveLab to leave some headroom.