So actually had kind of a similar thing happen to me the other day, as outlined in this post:
Although in looking into it further, it seems that this may not be the correct fix, as described here:
I’m not sure which one is the correct answer. In my experience over the last few days you have to do BOTH JucePlugin_PreferredChannelConfigurations AND isBusesLayoutSupported for VST/AU to work correctly in all cases, but this post seems to indicate otherwise?