A similar issue was reported recently:
The way that AudioUnits handle their channel remapping was tweaked a bit, but this can cause issues for plugins that were expecting unused input channels to be empty.
The boilerplate plugin project contains some code to clear unused output channels:
// In case we have more outputs than inputs, this code clears any output
// channels that didn't contain input data, (because these aren't
// guaranteed to be empty - they may contain garbage).
// This is here to avoid people getting screaming feedback
// when they first compile a plugin, but obviously you don't need to keep
// this code if your algorithm always overwrites all the output channels.
for (auto i = totalNumInputChannels; i < totalNumOutputChannels; ++i)
buffer.clear (i, 0, buffer.getNumSamples());
Do you have something like this in your processBlock?